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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id>
<journal-title>Frontiers in Microbiology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Microbiol.</abbrev-journal-title>
<issn pub-type="epub">1664-302X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fmicb.2021.732458</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Microbiology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Whole-Genome and Transcriptome Sequencing of <italic>Phlebopus portentosus</italic> Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Wan</surname> <given-names>Jia-Ning</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="author-notes" rid="fn002"><sup>&#x2020;</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Li</surname> <given-names>Yan</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="author-notes" rid="fn002"><sup>&#x2020;</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Guo</surname> <given-names>Ting</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Ji</surname> <given-names>Guang-Yan</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Luo</surname> <given-names>Shun-Zhen</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Ji</surname> <given-names>Kai-Ping</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>&#x002A;</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Cao</surname> <given-names>Yang</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Tan</surname> <given-names>Qi</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/729699/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Bao</surname> <given-names>Da-Peng</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/508754/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Yang</surname> <given-names>Rui-Heng</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="corresp" rid="c002"><sup>&#x002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/910886/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences</institution>, <addr-line>Shanghai</addr-line>, <country>China</country></aff>
<aff id="aff2"><sup>2</sup><institution>Hongzhen Agricultural Science and Technology Co. Ltd.</institution>, <addr-line>Jinghong</addr-line>, <country>China</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Baolei Jia, Chung-Ang University, South Korea</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Shireesh Srivastava, International Centre for Genetic Engineering and Biotechnology, India; Lujiang Hao, Qilu University of Technology, China; Yee Shin Tan, University of Malaya, Malaysia</p></fn>
<corresp id="c001">&#x002A;Correspondence: Kai-Ping Ji, <email>jkpcnlc@126.com</email></corresp>
<corresp id="c002">Rui-Heng Yang, <email>yangrh@saas.sh.cn</email></corresp>
<fn fn-type="equal" id="fn002"><p><sup>&#x2020;</sup>These authors have contributed equally to this work</p></fn>
<fn fn-type="other" id="fn004"><p>This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>29</day>
<month>09</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>12</volume>
<elocation-id>732458</elocation-id>
<history>
<date date-type="received">
<day>29</day>
<month>06</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>03</day>
<month>09</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2021 Wan, Li, Guo, Ji, Luo, Ji, Cao, Tan, Bao and Yang.</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Wan, Li, Guo, Ji, Luo, Ji, Cao, Tan, Bao and Yang</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<abstract>
<p>Phlebopus <italic>portentosus</italic> (Berk. and Broome) Boedijin, a widely consumed mushroom in China and Thailand, is the first species in the order Boletaceae to have been industrially cultivated on a large scale. However, to date, the lignocellulose degradation system and molecular basis of fruiting body development in <italic>P. portentosus</italic> have remained cryptic. In the present study, genome and transcriptome sequencing of <italic>P. portentosus</italic> was performed during the mycelium (S), primordium (P), and fruiting body (F) stages. A genome of 32.74 Mb with a 48.92% GC content across 62 scaffolds was obtained. A total of 9,464 putative genes were predicted from the genome, of which the number of genes related to plant cell wall-degrading enzymes was much lower than that of some saprophytic mushrooms with specific ectomycorrhizal niches. Principal component analysis of RNA-Seq data revealed that the gene expression profiles at all three stages were different. The low expression of plant cell wall-degrading genes also confirmed the limited ability to degrade lignocellulose. The expression profiles also revealed that some conserved and specific pathways were enriched in the different developmental stages of <italic>P. portentosus</italic>. Starch and sucrose metabolic pathways were enriched in the mycelium stage, while DNA replication, the proteasome and MAPK signaling pathways may be associated with maturation. These results provide a new perspective for understanding the key pathways and hub genes involved in <italic>P. portentosus</italic> development.</p>
</abstract>
<kwd-group>
<kwd>ectomycorrhizal fungi</kwd>
<kwd>genome</kwd>
<kwd>transcriptome</kwd>
<kwd>CAZymes</kwd>
<kwd>plant cell wall degradation</kwd>
</kwd-group>
<counts>
<fig-count count="7"/>
<table-count count="4"/>
<equation-count count="0"/>
<ref-count count="80"/>
<page-count count="16"/>
<word-count count="12131"/>
</counts>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="S1">
<title>Introduction</title>
<p><italic>Phlebopus portentosus</italic> (Berk. and Broome) Boedijin is an ectomycorrhizal edible mushroom with a widespread distribution in tropical parts of China, especially Yunnan, Guangxi, and Hainan provinces (<xref ref-type="bibr" rid="B76">Zhang et al., 2017</xref>). Because it is rich in nutrients, e.g., polysaccharides, amino acids, mineral elements, and pyrrole alkaloids, this fungus is popular and widely used in these regions (<xref ref-type="bibr" rid="B56">Sanmee et al., 2010</xref>; <xref ref-type="bibr" rid="B62">Sun et al., 2018</xref>; <xref ref-type="bibr" rid="B30">Kumla et al., 2021</xref>). <italic>P. portentosus</italic> has been successfully artificially cultivated and produces sporocarps in artificial substances <italic>in vitro</italic> in greenhouses or factories in China and Thailand, making it the first species in the order Boletaceae to have been industrially cultivated on a large scale (<xref ref-type="bibr" rid="B24">Ji et al., 2011</xref>; <xref ref-type="bibr" rid="B28">Kumla et al., 2015</xref>; <xref ref-type="bibr" rid="B76">Zhang et al., 2017</xref>). Especially in China, the industrialized cultivation of <italic>P. portentosus</italic> is highly similar to the <italic>Agaricus</italic> mushroom industry, with a daily production of 6 tons (<xref ref-type="bibr" rid="B76">Zhang et al., 2017</xref>). Nutrition and management techniques play important roles in maintaining the yields and quality of mushrooms (<xref ref-type="bibr" rid="B65">Tseng and Luong, 1984</xref>). Furthermore, understanding the lignocellulose degradation system and fruiting body development of this fungus is crucial to enhance yields and improving quality (<xref ref-type="bibr" rid="B21">Isikhuemhen and Mikiashvilli, 2009</xref>). However, the molecular basis of these biological processes is not fully understood.</p>
<p>Although <italic>P. portentosus</italic> can be cultivated by providing carbon or nitrogen compounds in artificial media, it is still characterized as an ectomycorrhizal (ECM) fungus that requires the use of coculture and isotopic methods (<xref ref-type="bibr" rid="B49">Pham et al., 2012</xref>; <xref ref-type="bibr" rid="B29">Kumla et al., 2016</xref>). Because most ectomycorrhizal fungi have difficulty producing macroscopic sporocarps in axenic culture on a large scale (<xref ref-type="bibr" rid="B16">Hall et al., 2003</xref>), some studies have revealed that two ecological niches may be required for <italic>P. portentosus</italic> growth, both independently as a saprophyte and in association with plants as an ectomycorrhizal symbiont, offering an excellent model to study the mechanisms by which fungi obtain nutrition from <italic>in vitro</italic> environments (<xref ref-type="bibr" rid="B7">Cao et al., 2015</xref>; <xref ref-type="bibr" rid="B76">Zhang et al., 2017</xref>). Plant cell wall-degrading enzymes (PCWDEs) secreted by fungi, including cellulases, hemicellulases, pectinases, and ligninases, provide fungi with the means to acquire energy and nutrients from plant cell walls (<xref ref-type="bibr" rid="B17">Hammel, 1997</xref>). However, genomic and transcriptomic comparisons between ectomycorrhizal and saprophytic fungi have revealed a reduced repertoire of genes encoding PCWDEs in ectomycorrhizal fungi, resulting in a limited capacity to decompose lignocellulose (<xref ref-type="bibr" rid="B27">Kohler et al., 2015</xref>; <xref ref-type="bibr" rid="B43">Miyauchi et al., 2020</xref>). A genome analysis of <italic>P. portentosus</italic> also revealed the presence of few or no copies of carbohydrate metabolism enzymes (CAZymes) that act on cellulose, xylan, pectin, and lignin (<xref ref-type="bibr" rid="B7">Cao et al., 2015</xref>). It is surprising that so few genes for lignocellulose degradation support <italic>P. portentosus</italic> growth on sawdust substances. However, our understanding of these enzymatic repertoires of <italic>P. portentosus</italic> is far from complete.</p>
<p>The hyphal differentiation, fruiting body formation and development of edible mushrooms are complex processes. The expression of genes at different stages of fungal development (hyphae, primordia, and fruiting body) is associated with yield and quality. Thus, an understanding of the molecular mechanisms regulating fruiting body development is necessary to generate improved strains and varieties of mushrooms by genetic modification or breeding. With the advent of next-generation sequencing techniques, genome and transcriptome sequencing of saprophytic and ectomycorrhizal mushrooms has been widely used to assess gene expression in different growth stages, including for <italic>Agrocybe aegerita</italic> (<xref ref-type="bibr" rid="B68">Wang et al., 2013</xref>), <italic>Lentinula edodes</italic> (<xref ref-type="bibr" rid="B61">Song et al., 2018</xref>; <xref ref-type="bibr" rid="B69">Wang et al., 2018</xref>), <italic>Flammulina velutipes</italic> (<xref ref-type="bibr" rid="B35">Liu et al., 2020</xref>), <italic>Pleurotus eryngii</italic> (<xref ref-type="bibr" rid="B72">Xie et al., 2018</xref>), <italic>Morchella</italic> (<xref ref-type="bibr" rid="B18">Hao et al., 2019</xref>; <xref ref-type="bibr" rid="B70">Wei et al., 2019</xref>), and <italic>Tricholoma matsutake</italic> (<xref ref-type="bibr" rid="B64">Tang et al., 2020</xref>). Stage-specific pathways enriched and correlated with the growth and development of fruiting bodies have been identified, with functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins. Although <italic>P. portentosus</italic> has been successfully artificially cultivated, gene expression in this fungus grown <italic>in vitro</italic> during different developmental stages is poorly understood.</p>
<p>To better understand the molecular mechanism of lignocellulose degradation and fruiting body development, whole-genome and transcriptome sequencing of <italic>P. portentosus</italic> was performed. Three developmental stages were analyzed, including hyphal, primordia, and fruit body stages. The results of genomic and transcriptomic analyses will improve our understanding of the stage-specific expression of genes associated with the functional properties of fruiting body development in <italic>P. portentosus</italic>. In addition, the transcriptomic profiles of ectomycorrhizal (ECM) fungi cultivated <italic>in vitro</italic> provide a foundation for further research on the cultivation of other ectomycorrhizal (ECM) fungi.</p>
</sec>
<sec id="S2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="S2.SS1">
<title>Strain Collection, Artificial Cultivation and Monokaryotic Strain Preparation</title>
<p>The strain PP17026, which was collected from Yunnan Province, China, was provided by Hongzhen Agricultural Science and Technology Co. Ltd. and cultured on M1 medium in the dark at 30&#x00B0;C. Spawn preparation, artificial cultivation and management of <italic>P. portentosus</italic> was performed according to previously published methods (<xref ref-type="bibr" rid="B73">Yang et al., 2019</xref>). Samples were collected in the hyphal (S, stage III), primordia (P, stage VI), and fruiting body (F, stage VII) stages (<xref ref-type="bibr" rid="B73">Yang et al., 2019</xref>). The hyphae fully covered on the surface of substrates, the small primordia with about 0.2 cm height and the stipes and pileus (cut into 0.2 cm &#x00D7; 0.2 cm pieces) used as representative samples of S, P, and F stages respectively were collected and flash-frozen in liquid nitrogen and stored at &#x2013;80&#x00B0;C before RNA extraction.</p>
<p>The monokaryotic protoplasts were isolated from PP17026 using a previously published method (<xref ref-type="bibr" rid="B8">Chang et al., 1985</xref>). After 10 days of incubation, mycelia were collected and stored at &#x2013;80&#x00B0;C until DNA and RNA extraction for genome and transcriptome sequencing. Transcriptome sequencing of monokaryotic strains was performed to correct the gene prediction results from the genome annotation.</p>
</sec>
<sec id="S2.SS2">
<title>DNA Extraction, Library Construction and Genome Sequencing</title>
<p>DNA was extracted from the monokaryotic strain using the CTAB method. A total of 100&#x2013;200 mg wet weight mycelium was ground in liquid nitrogen using a pestle in a centrifugal tube. Then, 1.5 mL of extraction buffer was added containing 20 mM EDTA, 100 mM Tris-HCl, 1.5 M NaCl, 2% CTAB, and 1% &#x03B2;-mercaptoethanol, and the sample was incubated at 65&#x00B0;C for 30 min. Protein and polysaccharide removal and DNA precipitation were conducted using chloroform-isoamyl alcohol (24:1, v/v) and isopropanol, respectively. The concentration, purity and integrity of DNA were assessed by NanoDrop (Thermo Scientific), Qubit and pulsed field electrophoresis analysis, respectively. A 20-kb sequencing library was built using large DNA segments with an ONT Template prep kit (SQK-LSK109) and an NEB Next FFPE DNA Repair Mix kit. The high-quality library was sequenced on an ONT PromethION platform with a corresponding R9 cell and an ONT sequencing reagent kit (EXP-FLP001.PRO.6). In addition, a small 300-bp sequencing library was built for the Illumina platform to improve the accuracy of the long-fragment library sequencing results.</p>
</sec>
<sec id="S2.SS3">
<title>RNA Extraction, Library Construction and RNA Sequencing</title>
<p>Total RNA were extracted from all samples as previously described using TRIzol reagent (Invitrogen, Burlington, ON, Canada). Three biological replicates were processed. The purity and concentration of RNA was assessed using a NanoPhotometer<sup>&#x00AE;</sup> spectrophotometer (IMPLEN, CA, United States) and a Qubit<sup>&#x00AE;</sup> RNA Assay Kit with a Qubit<sup>&#x00AE;</sup>2.0 Flurometer (Life Technologies, CA, United States). RNA integrity was assessed using an RNA Nano 6000 Assay Kit with the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, United States). Subsequently, RNA was treated with DNase I (Thermo Fisher, Waltham, MA, United States), and the mRNA was purified based on PolyA selection and fragmentation. First strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) followed by second strand cDNA synthesis, end repair, 30-end adenylation, adapter ligation and PCR amplification. Purification was performed using AmPureXP Beads (Beckman Coulter, Brea, CA, United States). The 300 bp libraries were sequenced for paired-end 150-bp-reads on Illumina HiSeq Novaseq 6000 platform (Illumina Inc., United States).</p>
</sec>
<sec id="S2.SS4">
<title>Genome Assembly and Annotations</title>
<p>To retrieve the nucleotide sequences from raw signal data generated from the ONT platform, base calling was performed using Albacore implemented in MinKNOW (<xref ref-type="bibr" rid="B55">Sahoo, 2017</xref>). Subsequently, by filtering the low-quality reads and demultiplexing the ONT barcodes and short reads, the filtered subreads were obtained using Canu v1.5 (<xref ref-type="bibr" rid="B57">Sergey et al., 2017</xref>). Raw Illumina data trimming was performed according to previously published methods (<xref ref-type="bibr" rid="B74">Yang et al., 2016</xref>). The corrected subreads were assembled into contigs using wtdbg v1.2.8 (<xref ref-type="bibr" rid="B54">Ruan and Li, 2020</xref>). To improve assembly, contig correction with Illumina read data was performed using Pilon (<xref ref-type="bibr" rid="B67">Walker et al., 2014</xref>). The completeness of the genome assembly was evaluated using BUSCO 4.0 with fungi_odb9 (<xref ref-type="bibr" rid="B60">Sim&#x00E3;o et al., 2015</xref>). MicroRNAs, rRNAs, and tRNAs were identified using tRNAscan-SE (<xref ref-type="bibr" rid="B37">Lowe and Eddy, 1997</xref>) and Infernal 1.1 (<xref ref-type="bibr" rid="B44">Nawrocki, 2014</xref>).</p>
<p>Three methods were used for gene prediction: (i) using a combination of the results from Genscan (<xref ref-type="bibr" rid="B6">Burge and Karlin, 1998</xref>), Augustus v2.4 (<xref ref-type="bibr" rid="B40">Mario and Burkhard, 2005</xref>), GlimmerHMM v3.0.4 (<xref ref-type="bibr" rid="B39">Majoros et al., 2004</xref>), GeneID v1.4 (<xref ref-type="bibr" rid="B3">Blanco et al., 2002</xref>), and SNAP (version 2006-07-28) (<xref ref-type="bibr" rid="B20">Ian, 2004</xref>); (ii) homologous protein prediction conducted using GeMoMa v1.3.1 (<xref ref-type="bibr" rid="B23">Jens et al., 2019</xref>); and (iii) unigenes were assembled and predicted using Hisat2 v2.0.4 (<xref ref-type="bibr" rid="B25">Kim et al., 2019</xref>), StringTie v1.2.3 (<xref ref-type="bibr" rid="B48">Pertea et al., 2015</xref>) and TransDecoder v2.0 based on the transcriptome sequencing of monokaryotic strains. All three results were integrated using EVM v1.1.1 to obtain an accurate prediction (<xref ref-type="bibr" rid="B15">Haas et al., 2008</xref>). Predicted genes were annotated using BLAST (Basic Local Alignment Search Tool) searches against Swiss-Prot (<xref ref-type="bibr" rid="B5">Boeckmann et al., 2005</xref>), TrEMBL (<xref ref-type="bibr" rid="B52">R&#x00E9;dei, 2008</xref>) and Nr databases. Gene ontology and KEGG metabolic pathway matches were identified using local Blast2GO tools (<xref ref-type="bibr" rid="B11">Conesa et al., 2005</xref>) and KAAS (<xref ref-type="bibr" rid="B75">Yuki et al., 2007</xref>), respectively. All predicted protein families were analyzed with InterProScan (<xref ref-type="bibr" rid="B51">Quevillon et al., 2005</xref>) and Pfam analysis (<xref ref-type="bibr" rid="B13">Finn et al., 2010</xref>). Carbohydrate-active enzymes were annotated using dbCAN (<xref ref-type="bibr" rid="B19">Huang et al., 2018</xref>). Oxidoreductases were extracted from the proteins predicted from the genome using a combination of IPR domain searches and the JGI cluster pipeline<sup><xref ref-type="fn" rid="footnote1">1</xref></sup> according to a previously published method (<xref ref-type="bibr" rid="B14">Floudas et al., 2012</xref>). The A- and B-mating-type genes were identified using previously published methods (<xref ref-type="bibr" rid="B9">Chen et al., 2016</xref>). The genome has been submitted to the NCBI under the accession numbers of <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JAHRGP000000000">JAHRGP000000000</ext-link>.</p>
</sec>
<sec id="S2.SS5">
<title>Data Processing, Alignment With the Reference Genome, Differentially Expressed Gene Analysis and Annotations for RNA Sequencing</title>
<p>The 150 bp paired-end reads obtained from the RNA-Seq analysis were trimmed using SeqPrep and Sickle to remove adaptor sequences, low-quality reads (those with ambiguous nucleotides and quality scores &#x003C; 20). The filtered reads were mapped to the genome using HISAT2 v2.0.4. Transcripts were assembled and reconstructed using StringTie based on the HISAT2 mapping files. Several databases were used to annotate gene functions, including the Nr (NCBI non-redundant protein sequences), Nt (NCBI non-redundant nucleotide sequences), KOG/COG (Eukaryotic Ortholog Groups/Clusters of Orthologous Groups of proteins), Swiss-Prot (a manually annotated and reviewed protein sequence database), KO (KEGG Ortholog) and GO (Gene Ontology) databases. Gene expression was normalized using the FPKM (fragments per kilobase of transcript million mapped reads) method. The differentially expressed genes (DEGs) across all the samples were identified using DESeq2 (<xref ref-type="bibr" rid="B36">Love et al., 2014</xref>). Genes showing at least a twofold gene expression change with an FDR value &#x003C; 0.05 were considered significantly differentially expressed. GO (Fisher&#x2019;s exact test with corrected <italic>P</italic>-value &#x003C; 0.05) and KEGG (Fisher&#x2019;s exact test with corrected <italic>P</italic>-value &#x003C; 0.05) enrichment analyses of DEGs associated with the significantly up- and downregulated genes between different stages were performed using Goatools (<xref ref-type="bibr" rid="B26">Klopfenstein et al., 2018</xref>) and R packages (<xref ref-type="bibr" rid="B46">Oksanen et al., 2011</xref>), respectively. Venn, PCA and hierarchical clustering for all correlation analyses were conducted using R packages. Weighted gene coexpression network analysis (WGCNA) was performed according to the method published previously (<xref ref-type="bibr" rid="B33">Li et al., 2019</xref>).</p>
</sec>
<sec id="S2.SS6">
<title>Quantitative Reverse Transcription (RT)-Polymerase Chain Reaction (PCR) and Semiquantitative RT-PCR</title>
<p>For each sample, 1 &#x03BC;g of RNA was used for cDNA synthesis using a TAKARA PrimeScript RT Reagent Kit. Semiquantitative SYBR green-based RT-PCR was performed using SYBR Premix Ex TaqII (Tli RNaseH Plus). Alpha-<italic>Tubulin</italic> was used as the internal control for normalization. Detailed information for the primers used in the present study is listed in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table 1</xref>. The presented data are representative of three biological replicates and four technical replicates for each sample. Relative gene expression levels were calculated with the comparative threshold cycle method using a StepOne Plus Real Time PCR System (Applied Biosystems, United States).</p>
</sec>
<sec id="S2.SS7">
<title>Optimization of Culture Medium for <italic>Phlebopus portentosus</italic></title>
<p>The medium was optimized based on the results from the genome and transcriptome for suitable carbon sources selection. Stock cultures were grown on complete yeast extract medium (CYM) plates with 2% glucose, 0.2% yeast extracts, 0.2% peptone, 0.1% K<sub>2</sub>HPO<sub>4</sub>, 0.05% MgSO<sub>4</sub>, 0.046% KH<sub>2</sub>PO<sub>4</sub>, and 2% agar. All optimization experiments were carried out in 9-cm-diameter Petri dishes (16 ml/petri dish) with modified CYM medium containing 2% different carbon sources. All the samples cultivated at 30&#x00B0;C in the dark for 30 days. The measurement of hyphal diameters was conducted. The significance of growth rate on different carbon sources was determined using <italic>t-test</italic>.</p>
</sec>
</sec>
<sec sec-type="results" id="S3">
<title>Results</title>
<sec id="S3.SS1">
<title>Genome Assembly</title>
<p>Two sequencing libraries (ONT and Illumina) were constructed for the monokaryotic strain for genome assembly. A total of 951,686 long reads (11,348,781,309 bp) were generated using the ONT platform. The N50 and N90 values of the raw data were 18,704 and 6,226 bp, respectively. After filtering the low-quality reads, 792,451 reads (10,603,105,695 bp) were obtained, with N50, N90 and a mean length of reads 18,866, 7,033 and 13,380 bp. The total data provided 323-fold coverage of the genome (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 2</xref>). Illumina sequencing yielded a total of 5.56 Gb clean data, and 20,876,612 clean reads (6,208,784,986 bp) for the monokaryotic strain were obtained by RNA-Seq.</p>
<p>An assembly of 32,742,503 bp across 62 scaffolds with a GC content of 48.92% was obtained (<xref ref-type="table" rid="T1">Table 1</xref>). Based on the results from the BUSCOO pipeline, only 9 of 290 single-copy entries were missing, suggesting &#x003E; 95.17% genome completeness. Finally, 9,464 putative genes were predicted using a combination of different pipelines (<xref ref-type="table" rid="T1">Table 1</xref>). A total of 3393, 3175, 5143, 6751, 5552, 9023, and 9231 encoded proteins were identified with homologous sequences in the GO, KEGG, KOG, Pfam, SwissProt, TrEMBL, and Nr databases, respectively (<xref ref-type="table" rid="T1">Table 1</xref>). The 103 tRNA genes are dispersed in the genome. However, no rRNA genes were identified. Compared with other fungi used in this study, the genome size of <italic>P. portentosus</italic> was the smallest and the number of genes was the least except <italic>Tuber melanosporum</italic> (<xref ref-type="table" rid="T2">Table 2</xref>).</p>
<table-wrap position="float" id="T1">
<label>TABLE 1</label>
<caption><p>Statistical information associated with the genome sequenced in this study.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left"></td>
<td/>
<td valign="top" align="center">Value</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><bold>Genome size (bp)</bold></td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center"><bold>32,742,503</bold></td>
</tr>
<tr>
<td valign="top" align="left">Scaffolds</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">62</td>
</tr>
<tr>
<td valign="top" align="left">Scaffold N50 (bp)</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">1,263,687</td>
</tr>
<tr>
<td valign="top" align="left">GC (%)</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">48.92</td>
</tr>
<tr>
<td valign="top" align="left">No. of Genes</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">9464</td>
</tr>
<tr>
<td valign="top" align="left">rRNA</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td valign="top" align="left">tRNA</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">103</td>
</tr>
<tr>
<td valign="top" align="left">Annotations</td>
<td valign="top" align="center">GO</td>
<td valign="top" align="center">3393</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">KEGG</td>
<td valign="top" align="center">3175</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">KOG</td>
<td valign="top" align="center">5143</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Pfam</td>
<td valign="top" align="center">6751</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Swissprot</td>
<td valign="top" align="center">5552</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">TrEMBL</td>
<td valign="top" align="center">9023</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Nr</td>
<td valign="top" align="center">9231</td>
</tr>
<tr>
<td valign="top" align="left">BUSCOs</td>
<td valign="top" align="center">Complete BUSCOs (C)</td>
<td valign="top" align="center">276 (95.17%)</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Complete and single-copy BUSCOs (S)</td>
<td valign="top" align="center">264 (91.03%)</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Complete and duplicated BUSCOs (D)</td>
<td valign="top" align="center">12 (4.14%)</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Fragmented BUSCOs (F)</td>
<td valign="top" align="center">5 (1.72%)</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Missing BUSCOs (M)</td>
<td valign="top" align="center">9 (3.10%)</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Total Lineage BUSCOs</td>
<td valign="top" align="center">290</td>
</tr>
</tbody>
</table></table-wrap>
<table-wrap position="float" id="T2">
<label>TABLE 2</label>
<caption><p>The total number of CAZyme families in different fungal genomes.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Ecology inches</td>
<td valign="top" align="center">Species</td>
<td valign="top" align="center">Genome size (Mb)</td>
<td valign="top" align="center">No. of genes</td>
<td valign="top" align="center">Accession numbers</td>
<td valign="top" align="center">AA</td>
<td valign="top" align="center">CBM</td>
<td valign="top" align="center">CE</td>
<td valign="top" align="center">GH</td>
<td valign="top" align="center">GT</td>
<td valign="top" align="center">PL</td>
<td valign="top" align="center">Total</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"></td>
<td valign="top" align="center"><italic>Phlebopus portentosus</italic></td>
<td valign="top" align="center">32,74</td>
<td valign="top" align="center">9,464</td>
<td valign="top" align="center">This study</td>
<td valign="top" align="center">57</td>
<td valign="top" align="center">19</td>
<td valign="top" align="center">47</td>
<td valign="top" align="center">110</td>
<td valign="top" align="center">62</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">301</td>
</tr>
<tr>
<td valign="top" align="left">Ectomycorrhizal</td>
<td valign="top" align="center"><italic>Amanita muscaria</italic></td>
<td valign="top" align="center">40.70</td>
<td valign="top" align="center">18,091</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMDV01000001">JMDV01000001</ext-link></td>
<td valign="top" align="center">77</td>
<td valign="top" align="center">19</td>
<td valign="top" align="center">61</td>
<td valign="top" align="center">109</td>
<td valign="top" align="center">68</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">338</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Paxillus involutus</italic></td>
<td valign="top" align="center">58.30</td>
<td valign="top" align="center">17,984</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JOMD00000000">JOMD00000000</ext-link></td>
<td valign="top" align="center">62</td>
<td valign="top" align="center">14</td>
<td valign="top" align="center">64</td>
<td valign="top" align="center">171</td>
<td valign="top" align="center">84</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">404</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Paxillus rubicundulus</italic></td>
<td valign="top" align="center">53.01</td>
<td valign="top" align="center">22,354</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMDR00000000">JMDR00000000</ext-link></td>
<td valign="top" align="center">47</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">39</td>
<td valign="top" align="center">108</td>
<td valign="top" align="center">61</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">273</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Piloderma croceum</italic></td>
<td valign="top" align="center">59.33</td>
<td valign="top" align="center">21,607</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMDN00000000">JMDN00000000</ext-link></td>
<td valign="top" align="center">87</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">71</td>
<td valign="top" align="center">160</td>
<td valign="top" align="center">76</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">417</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Pisolithus microcarpus</italic></td>
<td valign="top" align="center">53.03</td>
<td valign="top" align="center">21,104</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMDM00000000">JMDM00000000</ext-link></td>
<td valign="top" align="center">31</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">30</td>
<td valign="top" align="center">88</td>
<td valign="top" align="center">69</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">227</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Pisolithus tinctorius</italic></td>
<td valign="top" align="center">71.01</td>
<td valign="top" align="center">22,845</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMDO00000000">JMDO00000000</ext-link></td>
<td valign="top" align="center">42</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">38</td>
<td valign="top" align="center">87</td>
<td valign="top" align="center">69</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">241</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Scleroderma citrinum</italic></td>
<td valign="top" align="center">56.14</td>
<td valign="top" align="center">20,993</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMDU00000000">JMDU00000000</ext-link></td>
<td valign="top" align="center">56</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">43</td>
<td valign="top" align="center">101</td>
<td valign="top" align="center">63</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">271</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Suillus luteus</italic></td>
<td valign="top" align="center">37.01</td>
<td valign="top" align="center">18,419</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JMSM00000000">JMSM00000000</ext-link></td>
<td valign="top" align="center">57</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">42</td>
<td valign="top" align="center">131</td>
<td valign="top" align="center">66</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">309</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Tuber melanosporum</italic></td>
<td valign="top" align="center">124.95</td>
<td valign="top" align="center">7,496</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="CABJ00000000">CABJ00000000</ext-link></td>
<td valign="top" align="center">38</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">25</td>
<td valign="top" align="center">83</td>
<td valign="top" align="center">58</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">215</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Laccaria bicolor</italic></td>
<td valign="top" align="center">64.88</td>
<td valign="top" align="center">18,264</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="ABFE00000000">ABFE00000000</ext-link></td>
<td valign="top" align="center">51</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">49</td>
<td valign="top" align="center">149</td>
<td valign="top" align="center">67</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">336</td>
</tr>
<tr>
<td valign="top" align="left">Saprophytic</td>
<td valign="top" align="center"><italic>Schizophyllum commune</italic></td>
<td valign="top" align="center">38.48</td>
<td valign="top" align="center">13,189</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="ADMJ00000000">ADMJ00000000</ext-link></td>
<td valign="top" align="center">85</td>
<td valign="top" align="center">22</td>
<td valign="top" align="center">82</td>
<td valign="top" align="center">241</td>
<td valign="top" align="center">77</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">525</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Lentinula edodes</italic></td>
<td valign="top" align="center">41.82</td>
<td valign="top" align="center">14,889</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="LDAT00000000">LDAT00000000</ext-link></td>
<td valign="top" align="center">90</td>
<td valign="top" align="center">40</td>
<td valign="top" align="center">80</td>
<td valign="top" align="center">249</td>
<td valign="top" align="center">78</td>
<td valign="top" align="center">10</td>
<td valign="top" align="center">547</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Volvariella volvacea</italic></td>
<td valign="top" align="center">36.45</td>
<td valign="top" align="center">11,084</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="AMXZ00000000">AMXZ00000000</ext-link></td>
<td valign="top" align="center">121</td>
<td valign="top" align="center">70</td>
<td valign="top" align="center">63</td>
<td valign="top" align="center">215</td>
<td valign="top" align="center">63</td>
<td valign="top" align="center">29</td>
<td valign="top" align="center">561</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Pleurotus ostreatus</italic></td>
<td valign="top" align="center">50.90</td>
<td valign="top" align="center">12,296</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="AYUK00000000">AYUK00000000</ext-link></td>
<td valign="top" align="center">139</td>
<td valign="top" align="center">61</td>
<td valign="top" align="center">79</td>
<td valign="top" align="center">233</td>
<td valign="top" align="center">69</td>
<td valign="top" align="center">25</td>
<td valign="top" align="center">606</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Coprinus cinereus</italic></td>
<td valign="top" align="center">38.70</td>
<td valign="top" align="center">16,862</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JAAGWA000000000">JAAGWA000000000</ext-link></td>
<td valign="top" align="center">132</td>
<td valign="top" align="center">67</td>
<td valign="top" align="center">86</td>
<td valign="top" align="center">192</td>
<td valign="top" align="center">74</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">567</td>
</tr>
<tr>
<td/>
<td valign="top" align="center"><italic>Agaricus bisporus</italic></td>
<td valign="top" align="center">30.23</td>
<td valign="top" align="center">10,448</td>
<td valign="top" align="center"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="AEOK00000000">AEOK00000000</ext-link></td>
<td valign="top" align="center">94</td>
<td valign="top" align="center">31</td>
<td valign="top" align="center">76</td>
<td valign="top" align="center">180</td>
<td valign="top" align="center">57</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">449</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn><p><italic>AA, auxiliary activity; CBM, carbohydrate-binding module; CE, carbohydrate esterase; GH, glycoside hydrolase; GT, glycosyl transferase; PL, polysaccharide lyase.</italic></p></fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="S3.SS2">
<title>Genome Annotations</title>
<p>Gene annotation and functional categorization were performed using EuKaryotic Orthologous Group (KOG), where 5143 genes were redundantly assigned into 25 categories (<xref ref-type="table" rid="T1">Table 1</xref> and <xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 1</xref>). Except for genes related to general function prediction only (R) and unknown function (S), the number of genes involved in posttranslational modification, protein turnover, and chaperones (O); signal transduction mechanisms (T); and translation, ribosomal structure and biogenesis (J) were the highest, reaching 551, 403, and 334, respectively. The genes assigned to defense mechanisms, nuclear structure, cell motility and extracellular structures were the least abundant, with only 37, 28, 6, and 5 identified, respectively.</p>
<p>In addition, 35.85% of total genes had at least one GO annotation. Within the cellular component (CC) category, 4604 genes were assigned to 11 subcategories, the most abundant being &#x201C;cell&#x201D; and &#x201C;cell part&#x201D; (<xref ref-type="table" rid="T1">Table 1</xref> and <xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 2</xref>). A total of 3035 genes were classified into 13 molecular function (MF) categories, the greatest number of which was catalytic activity, followed by binding. A total of 1,469 predicted genes were assigned to 13 biological process (BP) GO terms, the most heavily represented being metabolic process and cellular process.</p>
<p>A total of 3,175 genes involved in 108 pathways were detected by KEGG annotation. The most enriched pathways included biosynthesis of amino acids (111), ribosomes (111), RNA transport (109), carbon metabolism (98), spliceosome (92), and purine metabolism (84) (<xref ref-type="table" rid="T1">Table 1</xref> and <xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 3</xref>).</p>
</sec>
<sec id="S3.SS3">
<title>Carbohydrate Metabolism Enzymes Families</title>
<p>A total of 301 CAZyme-coding genes for plant cell wall degradation were detected in the <italic>P. portentosus</italic> genome. These genes were divided into six families, including 57 auxiliary activities (AA) family genes, 19 carbohydrate-binding module (CBM) family genes, 47 carbohydrate esterase (CE) family genes, 110 glycoside hydrolase (GH) family genes, 62 glycosyl transferase (GT) family genes, and 6 polysaccharide lyase (PL) family genes (<xref ref-type="table" rid="T2">Table 2</xref>). The total number of CAZyme family genes in <italic>P. portentosus</italic> was within the range of that observed for mycorrhizal fungi (<xref ref-type="table" rid="T2">Table 2</xref>). The average number (303) of CAZyme families detected in the genomes of ectomycorrhizal fungi was much lower (ranging from 215 in <italic>T. melanosporum</italic> to 417 in <italic>Piloderma croceum</italic>) than that of saprophytic fungi (average number 542, ranging from 449 in <italic>A. bisporus</italic> to 606 in <italic>P. ostreatus</italic>) (<xref ref-type="table" rid="T2">Table 2</xref>). The number of AAs in <italic>P. portentosus</italic> (57 copies) was similar to that observed in <italic>Paxillus involutus</italic> (62 copies). <italic>P. portentosus</italic> had the same number of genes (19) related to CBM families as <italic>Amanita muscaria</italic> (<xref ref-type="table" rid="T2">Table 2</xref>). The number of genes belonging to GH families predicted in <italic>P. portentosus</italic>, <italic>A. muscaria</italic>, and <italic>P. rubicundulus</italic> was 110, 109, and 108, respectively. No more than 10 copies of PL genes in mycorrhizal fungi were identified. Except for GT families, the number of AA-, CBM-, CE-, GH-, and PL-encoding genes was much lower in ectomycorrhizal fungi than in saprophytic fungi (<xref ref-type="table" rid="T2">Table 2</xref>).</p>
<p>Based on the compositions of CAZyme families, the clustering results revealed two clades that included either mycorrhizal or saprophytic fungi. The pattern of CAZyme genes in <italic>P. portentosus</italic> was similar to that observed in <italic>P. rubicundulus</italic>, <italic>P. involutus</italic>, and <italic>Suillus luteus</italic> (<xref ref-type="fig" rid="F1">Figure 1</xref>). The top five most abundant families in <italic>P. portentosus</italic> were CE10 (36 copies), GH16 (17 copies), AA7 (16 copies), AA1_1 (12 copies), and CBM5 (8 copies). CE10 genes encode esterases, GH16 enzymes act on xyloglucan and chitin and AA7 genes encode gluco- or chito-oligosaccharide oxidases, all of which were abundant in mycorrhizal and saprophytic fungi (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 1</xref>). AA1_1 enzymes are multicopper oxidases and represent the most abundant AA family in <italic>P. portentosus</italic> and mycorrhizal fungi assayed in the present study, while AA3_2 enzymes belonging to the glucose-methanol-choline (GMC) oxidoreductase family were the most abundant in saprophytic fungi (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 1</xref>). In addition, the families GH6 and GH7, which are involved in attacking crystalline cellulose, were present in all saprophytic fungi assayed in the present study and were absent in <italic>P. portentosus</italic> and other ectomycorrhizal fungi (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 1</xref>). The families GH13, GH15, GH27, and GH71 were enriched in <italic>P. portentosus</italic>, of which the copy numbers of the starch degradation-associated GH13, GH27, and GH71 families were higher than those observed in other mycorrhizal fungi (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 1</xref>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption><p>Heatmap clustering of mycorrhizal and saprophytic fungi based on genes related to CAZyme families and lignocellulose decomposition. <bold>(A)</bold> Heatmap clustering based on CAZyme families; <bold>(B)</bold> Heatmap clustering based on genes related to lignocellulose decomposition.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g001.tif"/>
</fig>
</sec>
<sec id="S3.SS4">
<title>Genes Involved in Lignocellulose Decomposition</title>
<p>Low copy numbers of genes were identified belonging to the cellulase, hemicellulase, pectinase, and lignin oxidase families, which directly act on lignocellulose and are listed in <xref ref-type="table" rid="T3">Table 3</xref>. Hierarchical clustering using the average-linkage method based on the composition of lignocellulases also resulted in the identification of two clades, revealing the different compositions of lignocellulases between ectomycorrhizal and saprophytic fungi (<xref ref-type="fig" rid="F1">Figure 1B</xref>).</p>
<table-wrap position="float" id="T3">
<label>TABLE 3</label>
<caption><p>The distribution of genes related to lignocellulose degradation in <italic>P. portentosus</italic> and other fungi.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left"></td>
<td valign="top" align="center">Enzyme</td>
<td valign="top" align="center">EC</td>
<td valign="top" align="center" colspan="6">Saprophytic</td>
<td valign="top" align="center" colspan="11">Ectomycorrhizal</td>
</tr>
<tr>
<td valign="top" align="left" colspan="3"></td>
<td valign="top" align="left" colspan="6"><hr/></td>
<td valign="top" align="left" colspan="11"><hr/></td>
</tr>
<tr>
<td/>
<td/>
<td/>
<td valign="top" align="center">SC</td>
<td valign="top" align="center">LE</td>
<td valign="top" align="center">PO</td>
<td valign="top" align="center">CC</td>
<td valign="top" align="center">VV</td>
<td valign="top" align="center">AB</td>
<td valign="top" align="center">PP</td>
<td valign="top" align="center">Lb</td>
<td valign="top" align="center">AM</td>
<td valign="top" align="center">PI</td>
<td valign="top" align="center">PR</td>
<td valign="top" align="center">PC</td>
<td valign="top" align="center">PM</td>
<td valign="top" align="center">PT</td>
<td valign="top" align="center">SCC</td>
<td valign="top" align="center">SL</td>
<td valign="top" align="center">TM</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Cellulase</td>
<td valign="top" align="center">Endo-beta-1,4-glucanase</td>
<td valign="top" align="center">EC:3.2.1.4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">1,4-&#x03B2;-cellobiosidase</td>
<td valign="top" align="center">EC:3.2.1.91</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">&#x03B2;-glucosidase</td>
<td valign="top" align="center">EC:3.2.1.21</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">6</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Total</td>
<td/>
<td valign="top" align="center">17</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">24</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">22</td>
<td valign="top" align="center">10</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">8</td>
</tr>
<tr>
<td valign="top" align="left">Hemicellulase</td>
<td valign="top" align="center">Endo-1,4-betaxylanase</td>
<td valign="top" align="center">EC:3.2.1.8</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">&#x03B2;-xylosidase</td>
<td valign="top" align="center">EC:3.2.1.37</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">&#x03B1;-glucuronidase</td>
<td valign="top" align="center">EC:3.2.1.131</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Acetylxylan esterase</td>
<td valign="top" align="center">EC:3.1.1.72</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">10</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Feruloyl esterase</td>
<td valign="top" align="center">EC:3.1.1.73</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">&#x03B1;-<sc>L</sc>-arabinofuranosidases</td>
<td valign="top" align="center">EC:3.2.1.55</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Total</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">29</td>
<td valign="top" align="center">10</td>
<td valign="top" align="center">23</td>
<td valign="top" align="center">39</td>
<td valign="top" align="center">40</td>
<td valign="top" align="center">20</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td valign="top" align="left">Pectinase</td>
<td valign="top" align="center">Pectin lyase</td>
<td valign="top" align="center">EC:4.2.2.10</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Pectate lyase</td>
<td valign="top" align="center">EC:4.2.2.2</td>
<td valign="top" align="center">10</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Pectinesterase</td>
<td valign="top" align="center">EC:3.1.1.11</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Polygalacturonase</td>
<td valign="top" align="center">EC:3.2.1.15</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Total</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">14</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">3</td>
</tr>
<tr>
<td valign="top" align="left">Lignin Oxidase</td>
<td valign="top" align="center">Multicopper oxidase</td>
<td valign="top" align="center">1.10.3.2</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">17</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">14</td>
<td valign="top" align="center">19</td>
<td valign="top" align="center">17</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">9</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">5</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Lignin peroxidase</td>
<td valign="top" align="center">1.11.1.14</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Manganese peroxidase</td>
<td valign="top" align="center">1.11.1.13</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Other peroxidase</td>
<td valign="top" align="center">1.11.1.16</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Total</td>
<td valign="top" align="center">-</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">22</td>
<td valign="top" align="center">22</td>
<td valign="top" align="center">20</td>
<td valign="top" align="center">21</td>
<td valign="top" align="center">14</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">20</td>
<td valign="top" align="center">17</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">5</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Aryl-alcohol oxidase</td>
<td valign="top" align="center">1.1.3.7</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">13</td>
<td valign="top" align="center">35</td>
<td valign="top" align="center">21</td>
<td valign="top" align="center">25</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">3</td>
</tr>
<tr>
<td valign="top" align="left">Lignin Degrading Auxiliary Enzyme</td>
<td valign="top" align="center">Glucose oxidase</td>
<td valign="top" align="center">1.1.3.4</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Alcohol oxidase</td>
<td valign="top" align="center">1.1.3.13</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Pyranose oxidase</td>
<td valign="top" align="center">1.1.3.10</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Vanillyl-alcohol oxidase</td>
<td valign="top" align="center">1.1.3.38</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Glyoxal oxidase</td>
<td valign="top" align="center">1.1.3.-</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Galactose oxidase</td>
<td valign="top" align="center">1.1.3.9</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">0</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Benzoquinone reductase</td>
<td valign="top" align="center">1.6.5.6</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">3</td>
<td valign="top" align="center">2</td>
<td valign="top" align="center">1</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">Total</td>
<td valign="top" align="center">&#x2013;</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">28</td>
<td valign="top" align="center">54</td>
<td valign="top" align="center">33</td>
<td valign="top" align="center">36</td>
<td valign="top" align="center">25</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">21</td>
<td valign="top" align="center">14</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">29</td>
<td valign="top" align="center">8</td>
<td valign="top" align="center">10</td>
<td valign="top" align="center">15</td>
<td valign="top" align="center">22</td>
<td valign="top" align="center">6</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn><p><italic>AS, <italic>Agaricus bisporus</italic>; AM, <italic>Amanita muscaria</italic>; CC, <italic>Coprinus cinereus</italic>; LB, <italic>Laccaria bicolor</italic>; LE, <italic>Lentinula edodes</italic>; PI, <italic>Paxillus involutus</italic>; PR, <italic>Paxillus rubicundulus</italic>; PP, <italic>Phlebopus portentosus</italic>; PC, <italic>Piloderma croceum</italic>; PM, <italic>Pisolithus microcarpus</italic>; PT, <italic>Pisolithus tinctorius</italic>; PO, <italic>Pleurotus ostreatus</italic>; SC, <italic>Schizophyllum commune</italic>; SCC, <italic>Scleroderma citrinum</italic>; SL, <italic>Suillus luteus</italic>; TM, <italic>Tuber melanosporum</italic>; VV, <italic>Volvariella volvacea.</italic></italic></p></fn>
</table-wrap-foot>
</table-wrap>
<p>Four cellulase genes were identified in the <italic>P. portentosus</italic> genome, including 1 endo-beta-1,4-glucanase and 3 &#x03B2;-glucosidases. However, 1,4-&#x03B2;-cellobiosidase, which specifically hydrolyzes 1,4-beta-<sc>D</sc>-glucosidic linkages, was absent in <italic>P. portentosus</italic> and other ectomycorrhizal fungi, suggesting that <italic>P. portentosus</italic> may also have a low capacity to degrade celluloses. A low copy number of genes related to hemicellulases was observed in <italic>P. portentosus</italic>, with only five hemicellulases (no higher than seven in other ectomycorrhizal fungi) detected compared to saprophytic fungi (ranging from 10 to 29). In particular, no hemicellulases were detected in <italic>S. citrinum</italic>. &#x03B1;-Glucuronidases were absent in all ectomycorrhizal fungi evaluated in the present study, whereas they were present in all assayed saprophytic fungi. In <italic>P. port</italic>entosus, no pectinase genes were identified, as was observed in <italic>A. muscaria</italic>. The number of pectinases in ectomycorrhizal fungi ranged from 0 to 6. In saprophytic fungi, the copy number of pectinases varied significantly in different species, e.g., 3 present in <italic>Coprinus cinereus</italic> and 16 present in <italic>Volvariella volvacea</italic>. In addition, pectate lyases, which were detected in all saprophytic fungi, were absent in ectomycorrhizal fungi.</p>
<p>Six multicopper oxidases and one manganese peroxidase were identified in <italic>P. portentosus</italic>, fewer than was observed in other ectomycorrhizal fungi belonging to Basidiomycota. The number of multicopper oxidases encoded by these fungi was not in agreement with their associated niches and detected in all the fungi. The same pattern of auxiliary enzymes (e.g., aryl-alcohol oxidase, glyoxal oxidase, and benzoquinone reductase) was observed in all the fungi assayed in the present study. Pyranose oxidase, vanillyl-alcohol oxidase and galactose oxidase were not detected in any of the ectomycorrhizal fungi, including <italic>P. portentosus</italic>, except for <italic>L. bicolor</italic>.</p>
</sec>
<sec id="S3.SS5">
<title>Gene Expression Profiles in Different Stages</title>
<p>To determine the gene expression patterns during <italic>P. portentosus</italic> development, 9 samples from 3 growth stages were used for RNA-Seq. The average number of raw reads was 51,592,958, ranging from 47,344,648 in sample S3 to 56,606,312 in sample F3 (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 3</xref>). After filtering, the average numbers of clean reads and total bases was 51,161,401 and 7,631,017,892, ranging from 46,876,694 and 6,987,544,020 in sample S3 to 56,203,088 and 8,367,222,043 in sample F3, respectively (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 3</xref>). More than 87.62% of the reads within each replicate could be mapped to the reference genome (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 3</xref>).</p>
<p>Using an FPKM cutoff value of 1, 8,556, 8,628 and 8,673 genes expressed in stages S, P, and F accounted for 90.40, 91.17, and 91.64% of the total predicted genes, respectively (<xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 4A</xref>). A total of 8,316 common genes were expressed in all three stages. According to the FPKM values in different stages (FPKM &#x003C; 10, 10&#x2013;100, and &#x003E;100), three gene categories were determined (<xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 4B</xref>). The majority of genes in all the samples showed moderate expression, with FPKM values ranging from 10 to 100 (<xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 4B</xref>). The F stage had the greatest number of expressed genes, while the S stage had the fewest. However, the F stage had the fewest highly expressed genes, while the P stage had the most. To determine the correlations among different stages, the nine samples were clustered into three groups based on principal component analysis, which revealed different patterns of gene expression across all stages (<xref ref-type="supplementary-material" rid="SM1">Supplementary Figure 5</xref>).</p>
</sec>
<sec id="S3.SS6">
<title>Differentially Expressed Genes Across Different Developmental Stages</title>
<p>Based on FPKM values (&#x003E;1), a corrected <italic>P</italic>-value of 0.05 and log2 (fold change) of 1 were set as the threshold for significantly different gene expression. A total of 4,921 DEGs were identified in comparisons between the three groups (S vs. P, S vs. F, and P vs. F) (<xref ref-type="fig" rid="F2">Figure 2</xref>). The number of DEGs between the S and P groups was the highest (3600), followed by the S vs. F (2508) and P vs. F (2235) comparisons (<xref ref-type="fig" rid="F2">Figure 2B</xref>). There were 353 common DEGs in all three growth stage comparisons, which were enriched in the carbohydrate metabolism and proteasome categories (<xref ref-type="fig" rid="F2">Figure 2B</xref>). The most unique DEGs (919) were observed between the S and P groups compared to the S vs. F (509) and P vs. F (422) comparisons (<xref ref-type="fig" rid="F2">Figure 2A</xref>). The numbers of downregulated genes in the S vs. P, S vs. F and P vs. F comparisons were higher than those of upregulated genes (<xref ref-type="fig" rid="F2">Figure 2A</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption><p>Analysis of DEGs between different developmental stages. <bold>(A)</bold> DEG distribution between two analyzed samples. The number of differentially expressed genes is indicated at the top of the histograms. <bold>(B)</bold> Venn diagrams comparing shared DEGs between the adjacent growth stages.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g002.tif"/>
</fig>
</sec>
<sec id="S3.SS7">
<title>Functional Classification of Differentially Expressed Genes</title>
<p>All the DEGs were assigned into three different functional GO categories and 41 subcategories, including biological process (BP, 15 subcategories), cellular component (CC, 11 subcategories) and molecular function (MF, 15 subcategories) (<xref ref-type="fig" rid="F3">Figure 3</xref>). The most enriched DEGs were assigned to catalytic activity (GO: 0003824) in all three comparisons. The DEGs in the S vs. P comparison were significantly enriched in drug metabolic process, mitochondrial protein complex and purine-containing compound biosynthetic process. Functional categories for the P vs. F comparison were significantly enriched for gene families associated with cytoplasmic part, organic substance biosynthetic process, cellular biosynthetic process and organic substance biosynthetic process.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption><p>GO functional classification of differentially expressed genes. The <italic>Y</italic> axis represents the GO terms, the upper <italic>X</italic> axis represents the number of DEGs assigned to GO terms, the basal <italic>X</italic> axis represents the <italic>p</italic>-adjusted value, the broken lines represent the number of DEGs in each GO term, and the bars represent the <italic>p</italic>-adjusted value. <bold>(A)</bold> The DEGs assigned to GO terms in the S vs. P comparison; <bold>(B)</bold> indicated the DEGs assigned to GO terms in the P vs. F comparison; <bold>(C)</bold> the DEGs assigned to GO terms in the S vs. F comparison.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g003.tif"/>
</fig>
<p>To further understand the molecular and biological functions of the DEGs, they were mapped to the KEGG database (<xref ref-type="fig" rid="F4">Figure 4</xref>). Pathway enrichment analysis revealed that proteasome and DNA replication were the most enriched in the S vs. P comparison. The ribosome pathway was the most significant pathway in the P vs. F comparison, with a <italic>P</italic>-value of nearly 0, following by DNA replication, oxidative phosphorylation, citrate cycle and peroxisome. Amino sugar and nucleotide sugar metabolism, peroxisome and cysteine and methionine metabolism were the most enriched in the S vs. F comparison.</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption><p>KEGG pathways of differentially expressed genes. The <italic>Y</italic> axis represents the KEGG pathways, the upper <italic>X</italic> axis represents the number of DEGs, the basal <italic>X</italic> axis represents the <italic>p</italic>-adjusted value, the broken lines represent the number of DEGs in each KEGG pathway, and the bars represent the <italic>p</italic>-adjusted value. <bold>(A)</bold> KEGG pathways of differentially expressed genes in the S vs. P comparison; <bold>(B)</bold> KEGG pathways of differentially expressed genes in the P vs. F comparison; <bold>(C)</bold> KEGG pathways of differentially expressed genes in the S vs. F comparison.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g004.tif"/>
</fig>
</sec>
<sec id="S3.SS8">
<title>Gene Coexpression Network Construction</title>
<p>WGCNA was conducted to uncover the coexpression profiles in successive developmental stages (<xref ref-type="fig" rid="F5">Figure 5</xref>). Eight different modules were identified with high correlation coefficients according to the similarity of expression patterns (<xref ref-type="supplementary-material" rid="SM2">Supplementary Tables 5</xref>&#x2013;<xref ref-type="supplementary-material" rid="SM2">12</xref>). To identify key genes specific to the S stage, the yellow module was analyzed and included a total of 858 genes. Amino sugar and nucleotide sugar metabolism, pyrimidine metabolism, biosynthesis of amino acids, purine metabolism and starch and sucrose metabolism were the most enriched pathways (<xref ref-type="supplementary-material" rid="SM2">Supplementary Table 5</xref>). Regarding the amino acids biosynthesis pathways, those involved in phenylalanine, tyrosine and tryptophan biosynthesis, histidine metabolism and glycine, serine and threonine metabolism were the most abundant (<xref ref-type="supplementary-material" rid="SM2">Supplementary Table 5</xref>). The turquoise and red modules (harboring 1,275 and 433 identified genes, respectively) were specific to the P stage, the number of genes in which was higher than was observed in other two stages. In this stage, RNA transport, cell cycle (DNA replication and meiosis), proteasome and spliceosome were the most enriched pathways (<xref ref-type="supplementary-material" rid="SM2">Supplementary Tables 6</xref>,<xref ref-type="supplementary-material" rid="SM2">7</xref>). The blue (63 genes) and black (63 genes) modules were highly associated with the F stage. Biosynthesis of amino acids, glutathione metabolism, peroxisome, glycerophospholipid metabolism and MAPK signaling pathway were the most enriched in this stage (<xref ref-type="supplementary-material" rid="SM2">Supplementary Tables 8</xref>,<xref ref-type="supplementary-material" rid="SM2">9</xref>).</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption><p>WGCNA of genes in different developmental stages in <italic>P. portentosus</italic>. Module-trait weighted correlations and corresponding <italic>P</italic>-values for the identified gene module and their developmental stages. The label color on the right represents the strength of correlation, from 1 (red) to &#x2013;1 (blue). Each column corresponds to a developmental stage. The eight modules and the number of module member genes are shown on the left panel. The boxes with different color indicated the significant correlation between the module eigengene and the stage.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g005.tif"/>
</fig>
</sec>
<sec id="S3.SS9">
<title>Differential Expression of Carbohydrate Metabolism Enzymes Families and Lignocellulose Decomposition-Related Genes</title>
<p>Of the 301 CAZyme genes predicted from the genome, 277, 286 and 288 genes were expressed in the S, P, and F stages, respectively (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 4</xref>). The most highly expressed CAZyme genes were different in the three stages (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 4</xref>). In the S stage, the top five families with the highest FPKM values were CBM13 (1872.75), GH16 (1230.55), GH128 (1168.78), CBM13 (923.36) and AA5_1 (532.96). In the P stage, AA2 (1391.67), GT4 (992.50), GH128 (867.38), AA3_2 (298.65) and CBM50 (288.51) were more highly expressed than other families. The families GH16 (6346.44), GH18 (1097.48), GH128 (1003.62), GT4 (969.11), and GT2_Glyco_trans_2_3 (660.98) were overrepresented in stage F. The high expression of the glycoside hydrolase families GH16, GH18 and GH128 in all three stages indicated that <italic>P. portentosus</italic> has a high potential for starch or xylan degradation.</p>
<p>A total of 106 and 78 DEGs annotated as CAZyme families were detected in the S vs. P and P vs. F comparisons, respectively (<xref ref-type="supplementary-material" rid="SM1">Supplementary Table 4</xref>). In the S vs. P comparison, out of the 106 identified DEGs, 46 were upregulated and 60 were downregulated. Compared to the S stage, CBM13, GH16, AA5_1, GH18, AA6, AA3_2, GH17, GH5_30 and GT2_Chitin_synth_1 were significantly downregulated and AA2, GT4 and GH71 were upregulated in the P stage. In the P vs. F comparison, 52 DEGs were upregulated, including GH16, GH18, GT2_Glyco_trans_2_3, GH13_1 and GH31, while 26 DEGs were downregulated, including AA2, GH16, CE10, GH16, and CE4.</p>
</sec>
<sec id="S3.SS10">
<title>Differential Expression of Genes Involved in Lignocellulose Decomposition</title>
<p>Twenty-four genes involved in lignocellulose decomposition were predicted from the <italic>P. portentosus</italic> reference genome, of which 15 genes were differentially expressed in the different developmental stages (<xref ref-type="table" rid="T4">Table 4</xref>). The most highly expressed genes involved in lignocellulose decomposition in all 3 stages included lignin oxidases (manganese peroxidase) and lignin-degrading auxiliary enzymes (alcohol oxidase, benzoquinone reductase), suggesting that <italic>P. portentosus</italic> has the potential to degrade lignin (<xref ref-type="table" rid="T4">Table 4</xref>). However, endo-beta-1,4-glucanase, which acts on cellulose, was expressed at low levels. Compared to that observed in the S stage, the expression of manganese peroxidase (EVM0004344) in the P stage was significantly upregulated (293.84 vs. 1391.67, respectively, a nearly fivefold increase) (<xref ref-type="table" rid="T4">Table 4</xref>), the expression of which subsequently decreased in the F stage. The RT-PCR results confirmed the observed expression profiles (<xref ref-type="fig" rid="F6">Figure 6A</xref>). Multicopper oxidase laccases (EVM0002770, EVM0008799, and EVM0004198) were expressed at the highest levels in the S stage (<xref ref-type="table" rid="T4">Table 4</xref> and <xref ref-type="fig" rid="F6">Figure 6B</xref>). The lignin-degrading auxiliary enzymes glyoxal oxidase (EVM0006667), benzoquinone reductase (EVM0006980 and EVM0009178) and glucose oxidase (EVM0003870) were more highly expressed in the P stage than in the S and F stages (<xref ref-type="table" rid="T4">Table 4</xref>). The expression of aryl-alcohol oxidase (EVM0008750) gradually increased with the development of fruiting bodies, peaking in the F stage (<xref ref-type="table" rid="T4">Table 4</xref>). Endo-beta-1,4-glucanase expression was lower in the S (11.68) and F (23.71) stages than in the P stage (46.76) (<xref ref-type="table" rid="T4">Table 4</xref>). The expression of &#x03B2;-glucosidase (EVM0002244) increased from stages P (29.79) to F (105.70) (<xref ref-type="table" rid="T4">Table 4</xref> and <xref ref-type="fig" rid="F6">Figure 6D</xref>). Endo-1,4-betaxylanase (EVM0003710), which acts on hemicellulose, was expressed at higher levels in the F stage than in the P and S stages (<xref ref-type="table" rid="T4">Table 4</xref> and <xref ref-type="fig" rid="F6">Figure 6C</xref>).</p>
<table-wrap position="float" id="T4">
<label>TABLE 4</label>
<caption><p>FPKM of DEGs annotated as lignocellulose degradation enzymes.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Class</td>
<td valign="top" align="center">Gene_id</td>
<td valign="top" align="center">Enzymes</td>
<td valign="top" align="center">CAZyme</td>
<td valign="top" align="center" colspan="3">FPKM</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"></td>
<td/>
<td/>
<td valign="top" align="center"><bold>Families</bold></td>
<td valign="top" align="center"><bold>S</bold></td>
<td valign="top" align="center"><bold>P</bold></td>
<td valign="top" align="center"><bold>F</bold></td>
</tr>
<tr>
<td valign="top" align="left">Cellulase</td>
<td valign="top" align="center">EVM0003710</td>
<td valign="top" align="center">Endo-beta-1,4-glucanase</td>
<td valign="top" align="center">GH9</td>
<td valign="top" align="center">11.68 &#x00B1; 1.74<italic>b</italic>&#x00A0;&#x00A0;</td>
<td valign="top" align="center">46.76 &#x00B1; 19.02<italic>a</italic></td>
<td valign="top" align="center">23.71 &#x00B1; 8.09<italic>a</italic><italic>b</italic></td>
</tr>
<tr>
<td/>
<td valign="top" align="center">EVM0002244</td>
<td valign="top" align="center">&#x03B2;-glucosidase</td>
<td valign="top" align="center">GH3</td>
<td valign="top" align="center">25.15 &#x00B1; 4.58<italic>b</italic>&#x00A0;&#x00A0;</td>
<td valign="top" align="center">29.79 &#x00B1; 13.71<italic>b</italic></td>
<td valign="top" align="center">105.70 &#x00B1; 29.30<italic>a</italic>&#x00A0;&#x00A0;</td>
</tr>
<tr>
<td valign="top" align="left">Hemicellulase</td>
<td valign="top" align="center">EVM0005879</td>
<td valign="top" align="center">Endo-1,4-betaxylanase</td>
<td valign="top" align="center">CBM5</td>
<td valign="top" align="center">&#x00A0;&#x00A0;&#x00A0;5.10 &#x00B1; 0.25<italic>a</italic><italic>b</italic></td>
<td valign="top" align="center">3.63 &#x00B1; 0.59<italic>b</italic></td>
<td valign="top" align="center">&#x00A0;9.77 &#x00B1; 1.86<italic>a</italic></td>
</tr>
<tr>
<td valign="top" align="left">Pectinase</td>
<td valign="top" align="center">EVM0009029</td>
<td valign="top" align="center">Polygalacturonase</td>
<td valign="top" align="center">GH43_30</td>
<td valign="top" align="center">51.62 &#x00B1; 18.11<italic>a</italic></td>
<td valign="top" align="center">16.89 &#x00B1; 12.02<italic>a</italic></td>
<td valign="top" align="center">&#x00A0;1.67 &#x00B1; 0.49<italic>b</italic></td>
</tr>
<tr>
<td valign="top" align="left">Lignin</td>
<td valign="top" align="center">EVM0004344</td>
<td valign="top" align="center">Manganese peroxidase</td>
<td valign="top" align="center">AA2</td>
<td valign="top" align="center">293.84 &#x00B1; 68.16<italic>b</italic>&#x00A0;</td>
<td valign="top" align="center">1391.67 &#x00B1; 320.55<italic>a</italic>&#x00A0;&#x00A0;</td>
<td valign="top" align="center">473.57 &#x00B1; 172.23<italic>b</italic></td>
</tr>
<tr>
<td valign="top" align="left">Oxidase</td>
<td valign="top" align="center">EVM0002770</td>
<td valign="top" align="center">Multicopper oxidase</td>
<td valign="top" align="center">AA1_1</td>
<td valign="top" align="center">118.32 &#x00B1; 40.67<italic>a</italic></td>
<td valign="top" align="center">4.22 &#x00B1; 2.22<italic>b</italic></td>
<td valign="top" align="center">6.99 &#x00B1; 0.55<italic>b</italic></td>
</tr>
<tr>
<td/>
<td valign="top" align="center">EVM0008799</td>
<td valign="top" align="center">Multicopper oxidase</td>
<td valign="top" align="center">AA1_1</td>
<td valign="top" align="center">15.60 &#x00B1; 3.39<italic>a</italic></td>
<td valign="top" align="center">1.51 &#x00B1; 0.36<italic>c</italic></td>
<td valign="top" align="center">5.44 &#x00B1; 0.12<italic>b</italic></td>
</tr>
<tr>
<td/>
<td valign="top" align="center">EVM0004198</td>
<td valign="top" align="center">Multicopper oxidase</td>
<td valign="top" align="center">AA1_1</td>
<td valign="top" align="center">&#x00A0;&#x00A0;&#x00A0;&#x00A0;&#x00A0;2.18 &#x00B1; 0.44<italic>a</italic><italic>b</italic></td>
<td valign="top" align="center">&#x00A0;1.94 &#x00B1; 1.03<italic>b</italic></td>
<td valign="top" align="center">4.95 &#x00B1; 0.24<italic>a</italic></td>
</tr>
<tr>
<td valign="top" align="left">Lignin</td>
<td valign="top" align="center">EVM0003870</td>
<td valign="top" align="center">Glucose oxidase</td>
<td valign="top" align="center">AA3_2</td>
<td valign="top" align="center">&#x00A0;267.35 &#x00B1; 82.40<italic>a</italic>&#x00A0;</td>
<td valign="top" align="center">43.04 &#x00B1; 19.44<italic>b</italic></td>
<td valign="top" align="center">33.42 &#x00B1; 25.87<italic>b</italic></td>
</tr>
<tr>
<td valign="top" align="left">Degrading</td>
<td valign="top" align="center">EVM0006667</td>
<td valign="top" align="center">Glyoxal oxidase</td>
<td valign="top" align="center">AA5_1</td>
<td valign="top" align="center">&#x00A0;&#x00A0;532.96 &#x00B1; 102.57<italic>a</italic></td>
<td valign="top" align="center">140.47 &#x00B1; 3.04<italic>b</italic>&#x00A0;&#x00A0;&#x00A0;&#x00A0;</td>
<td valign="top" align="center">310.52 &#x00B1; 88.23<italic>b</italic>&#x00A0;&#x00A0;</td>
</tr>
<tr>
<td valign="top" align="left">Auxiliary</td>
<td valign="top" align="center">EVM0006812</td>
<td valign="top" align="center">Glyoxal oxidase</td>
<td valign="top" align="center">AA5_1</td>
<td valign="top" align="center">&#x00A0;&#x00A0;1.72 &#x00B1; 0.46<italic>b</italic></td>
<td valign="top" align="center">&#x00A0;&#x00A0;&#x00A0;&#x00A0;3.10 &#x00B1; 0.62<italic>a</italic><italic>b</italic></td>
<td valign="top" align="center">4.06 &#x00B1; 0.38<italic>a</italic></td>
</tr>
<tr>
<td valign="top" align="left">Enzyme</td>
<td valign="top" align="center">EVM0006980</td>
<td valign="top" align="center">Benzoquinone reductase</td>
<td valign="top" align="center">AA6</td>
<td valign="top" align="center">447.79 &#x00B1; 91.82<italic>a</italic></td>
<td valign="top" align="center">&#x00A0;&#x00A0;43.71 &#x00B1; 12.46<italic>b</italic></td>
<td valign="top" align="center">21.42 &#x00B1; 7.32<italic>b</italic>&#x00A0;&#x00A0;</td>
</tr>
<tr>
<td/>
<td valign="top" align="center">EVM0009178</td>
<td valign="top" align="center">Benzoquinone reductase</td>
<td valign="top" align="center">AA6</td>
<td valign="top" align="center">187.93 &#x00B1; 28.24<italic>a</italic></td>
<td valign="top" align="center">&#x00A0;&#x00A0;103.21 &#x00B1; 23.98<italic>a</italic><italic>b</italic></td>
<td valign="top" align="center">60.87 &#x00B1; 24.63<italic>b</italic></td>
</tr>
<tr>
<td/>
<td valign="top" align="center">EVM0000957</td>
<td valign="top" align="center">Alcohol oxidase</td>
<td valign="top" align="center">AA3_3</td>
<td valign="top" align="center">110.40 &#x00B1; 26.76<italic>a</italic></td>
<td valign="top" align="center">&#x00A0;&#x00A0;46.95 &#x00B1; 11.80<italic>b</italic></td>
<td valign="top" align="center">&#x00A0;&#x00A0;&#x00A0;79.24 &#x00B1; 53.18<italic>a</italic><italic>b</italic></td>
</tr>
<tr>
<td/>
<td valign="top" align="center">EVM0008750</td>
<td valign="top" align="center">Aryl-alcohol oxidase</td>
<td valign="top" align="center">AA3_2</td>
<td valign="top" align="center">&#x00A0;&#x00A0;9.36 &#x00B1; 0.74<italic>c</italic></td>
<td valign="top" align="center">33.56 &#x00B1; 6.94<italic>b</italic></td>
<td valign="top" align="center">&#x00A0;68.21 &#x00B1; 4.58<italic>a</italic>&#x00A0;&#x00A0;&#x00A0;</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn><p><italic>Different lowercase letters above bars indicate a significant difference according to the Duncan&#x2019;s multiple range test (<italic>p</italic> &#x003C; 0.05).</italic></p></fn>
</table-wrap-foot>
</table-wrap>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption><p>Relative expression of some lignin oxidases and cellulases in different developmental stages of <italic>P. portentosus</italic> using RT-PCR. <bold>(A)</bold> Manganese peroxidase; <bold>(B)</bold> multicopper oxidase; <bold>(C)</bold> endo-beta-1,4-glucanase; <bold>(D)</bold> &#x03B2;-glucosidase. Different lowercase letters above bars indicate a significant difference according to the Duncan&#x2019;s multiple range test (<italic>p</italic> &#x003C; 0.05).</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g006.tif"/>
</fig>
</sec>
<sec id="S3.SS11">
<title>Optimization of Culture Medium</title>
<p>From the genome and transcriptome results, <italic>P. portentosus</italic> exhibited a limited ability to degrade lignocellulose. The gene families acting on starch, xylan and chitin were most abundant in the genome and showed high expression in all the stages. Unique carbon sources (starch, xylan, and chitin) were further used to screen the most suitable culture medium, glucose as a control. By measuring the growth diameter of mycelia after 30 days of cultivation, the growth rate of <italic>P. portentosus</italic> on starch and xylan was much faster than that on glucose and chitin (<xref ref-type="fig" rid="F7">Figure 7A</xref>). In addition to the growth rate, the morphology of the colonies also differed. Aerial mycelia of <italic>P. portentosus</italic> were much thicker, and pigmentation was stronger on glucose and starch than on xylan (<xref ref-type="fig" rid="F7">Figure 7B</xref>). However, the integrity of mycelial edges were much better on xylan than on glucose and starch (<xref ref-type="fig" rid="F7">Figure 7B</xref>). Thus, xylan and starch may be more suitable carbon sources for <italic>P. portentosus</italic> than chitin.</p>
<fig id="F7" position="float">
<label>FIGURE 7</label>
<caption><p>The growth rate and morphology of <italic>P. portentosus</italic> cultured on different carbon sources. <bold>(A)</bold> Growth rate; <bold>(B)</bold> morphology of <italic>P. portentosus</italic> on different carbon sources after 30 days of cultivation, <bold>(B1)</bold> glucose, <bold>(B2)</bold> starch, <bold>(B3)</bold> xylan, <bold>(B4)</bold> chitin. Different lowercase letters above bars indicate a significant difference according to the Duncan&#x2019;s multiple range test (<italic>p</italic> &#x003C; 0.05).</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-12-732458-g007.tif"/>
</fig>
</sec>
</sec>
<sec sec-type="discussion" id="S4">
<title>Discussion</title>
<p>As the first ectomycorrhizal fungus in the order Boletaceae to have been industrially cultivated at a large scale, <italic>P. portentosus</italic> has attracted extensive attention worldwide (<xref ref-type="bibr" rid="B76">Zhang et al., 2017</xref>). However, the molecular mechanisms associated with the ability of <italic>P. portentosus</italic> to promote plant cell wall degradation and fruiting body development remain ambiguous. Genomics and transcriptomics provide an unprecedented means of elucidating the developmental and metabolic biological aspects of mushrooms. In the present study, genome and transcriptome sequencing was conducted to identify CAZyme family genes and DEGs in different developmental stages of <italic>P. portentosus</italic>. The results revealed the presence of no or few copies of carbohydrate metabolism enzymes (CAZymes) acting on cellulose, xylan, pectin and lignin in <italic>P. portentosus</italic>, an ectomycorrhizal fungus (<xref ref-type="bibr" rid="B27">Kohler et al., 2015</xref>). Some conserved pathways related to the proteasome, DNA replication, ribosome pathway and amino acid metabolism processes were correlated with the development of fruiting bodies.</p>
<p>Ectomycorrhizal fungi are considered mutualists that trade host photoassimilates for nutrients (<xref ref-type="bibr" rid="B10">Clavel et al., 2021</xref>). ECM fungi have been reported to have evolved from saprotrophic fungi and exhibit an extensive loss of enzymatic repertoires for lignocellulose decomposition during the transition to mycorrhizal habits (<xref ref-type="bibr" rid="B27">Kohler et al., 2015</xref>). The use of coculture and isotopic methods revealed that <italic>P. portentosus</italic> can form ectomycorrhizal symbioses with plants (<xref ref-type="bibr" rid="B29">Kumla et al., 2016</xref>). However, this fungus can be artificially cultivated <italic>in vitro</italic>, and an improved understanding of the repertoires of PCWDEs in <italic>P. portentosus</italic> is needed to elucidate the mechanisms associated with nutrient acquisition <italic>in vitro</italic>.</p>
<p>The composition of lignocellulose-degrading systems harbored by <italic>P. portentosus</italic> revealed ECM characteristics. Members of the families GH6 and GH7, which degrade crystalline cellulose (<xref ref-type="bibr" rid="B1">Baldrian and Val&#x00E1;kov&#x00E1;, 2008</xref>; <xref ref-type="bibr" rid="B14">Floudas et al., 2012</xref>), are absent in <italic>P. portentosus</italic> and other ECM fungi assayed in the present study except <italic>Piloderma croceum</italic> (1 GH7 copy). In addition to GH6 and GH7, fewer AA9 lytic polysaccharide monooxygenases (2&#x2013;5 copies, LPMOs) were present in all the genomes of ectomycorrhizal fungi assayed in the present study than in white-rot or straw-rot fungi (11&#x2013;34). These results are in agreement with reports of ECM fungi belonging to Boletales, which have lost nearly all copies of GH6 and GH7 genes and have no more than five copies of AA9 LPMOs (<xref ref-type="bibr" rid="B27">Kohler et al., 2015</xref>). These results also suggested that ECM fungi, including <italic>P. portentosus</italic>, have a limited capacity to degrade cellulose. In addition, no genes related to pectin degradation were detected in <italic>P. portentosus</italic> and <italic>A. muscaria</italic>. The lack of pectinases in ECM fungi has also been demonstrated using omics analyses (<xref ref-type="bibr" rid="B27">Kohler et al., 2015</xref>). Genes encoding enzymes mediating the degradation of pectin were shown to be reduced or completely lost among EM <italic>Amanita</italic> (<xref ref-type="bibr" rid="B22">Jaqueline et al., 2018</xref>). Each species used in the study had a different repertoire of multicopper oxidase (MCO) genes, ranging from 4 to 13 in saprophytic fungi and from 5 to 19 in ECM fungi (<xref ref-type="bibr" rid="B4">B&#x00F6;deker et al., 2009</xref>; <xref ref-type="bibr" rid="B27">Kohler et al., 2015</xref>; <xref ref-type="bibr" rid="B58">Shah et al., 2016</xref>). Six laccases (MCO) were identified in the <italic>P. portentosus</italic> genome, higher than that observed for <italic>S. commune</italic> but lower than other ECM fungi (except <italic>T. melanosporum</italic>). In addition to the low copy number of lignocellulose-degrading genes observed in the <italic>P. portentosus</italic> genome, the RNA-seq analysis of the different stages showed the low expression of these genes, with measured FPKM values of half of these lignocellulose-degrading genes less than 10. These results were also in agreement with the characteristics of ectomycorrhizal fungi revealed by omics analyses in other studies, and ectomycorrhizal fungi have low potential to degrade lignocellulose (<xref ref-type="bibr" rid="B41">Martin et al., 2016</xref>; <xref ref-type="bibr" rid="B58">Shah et al., 2016</xref>; <xref ref-type="bibr" rid="B43">Miyauchi et al., 2020</xref>).</p>
<p>Although <italic>P. portentosus</italic> was shown to have few copies and low expression of lignocellulose enzymes, the expression of these genes was also dependent on the stage of mushroom development. The expression of endo-beta-1,4-glucanase, &#x03B2;-glucosidase and endo-1,4-betaxylanase was highest in the P or F stages, which may suggest that cellulase and hemicellulase genes are potentially correlated with fruiting body formation and maturation. These results are in agreement with those obtained for some white-rot or straw-rot mushrooms, e.g., <italic>A. bisporus</italic>, <italic>P. ostreatus</italic>, <italic>L. edodes</italic>, <italic>L. tigrinus</italic>, and <italic>G. lucidum</italic> (<xref ref-type="bibr" rid="B59">Shoji and Royse, 2001</xref>; <xref ref-type="bibr" rid="B32">Lechner and Papinutti, 2006</xref>; <xref ref-type="bibr" rid="B12">Elisashvili et al., 2008</xref>; <xref ref-type="bibr" rid="B61">Song et al., 2018</xref>; <xref ref-type="bibr" rid="B71">Wu et al., 2018</xref>; <xref ref-type="bibr" rid="B79">Zhou et al., 2018</xref>). The activities of multicopper oxidases (laccases) and most lignin-degrading auxiliary enzymes reached their maximum levels in the M stage, similar to other mushrooms (<xref ref-type="bibr" rid="B59">Shoji and Royse, 2001</xref>; <xref ref-type="bibr" rid="B32">Lechner and Papinutti, 2006</xref>; <xref ref-type="bibr" rid="B12">Elisashvili et al., 2008</xref>), suggesting the potential to degrade lignin during the mycelial growth phase. Manganese peroxidase activity was reported to be high during the colonization stage and decrease during the first primordia and fruiting body formation stages in some saprophytic mushrooms (<xref ref-type="bibr" rid="B66">Vel&#x00E1;zquez-Cede&#x00F1;o et al., 2002</xref>; <xref ref-type="bibr" rid="B12">Elisashvili et al., 2008</xref>). However, the relative expression of manganese peroxidases in <italic>P. portentosus</italic> was inconsistent with previous reports, reaching the highest levels in the primordia stage and then decreasing in the fruiting body formation stage. The expression patterns of these enzymes in <italic>P. portentosus</italic> need to be further studied.</p>
<p>Some conserved and specific pathways have been shown to be enriched in the different stages of mushroom development (<xref ref-type="bibr" rid="B68">Wang et al., 2013</xref>, <xref ref-type="bibr" rid="B69">2018</xref>; <xref ref-type="bibr" rid="B78">Zhang et al., 2015</xref>; <xref ref-type="bibr" rid="B61">Song et al., 2018</xref>; <xref ref-type="bibr" rid="B72">Xie et al., 2018</xref>; <xref ref-type="bibr" rid="B79">Zhou et al., 2018</xref>; <xref ref-type="bibr" rid="B18">Hao et al., 2019</xref>; <xref ref-type="bibr" rid="B70">Wei et al., 2019</xref>; <xref ref-type="bibr" rid="B64">Tang et al., 2020</xref>). Starch and sucrose metabolism pathways were enriched in the mycelial stage in <italic>P. portentosus</italic>, which were also specific to the hyphal stage of Chinese <italic>Cordyceps</italic> (<xref ref-type="bibr" rid="B33">Li et al., 2019</xref>). Starch and sucrose may be important carbon sources for the growth of mycelia. Cultivation using starch and xylan as substrates demonstrated that metabolism plays important roles in acquiring nutrient acquisition in <italic>P. portentosus</italic>. Some ectomycorrhizal fungi belonged to <italic>Amanita</italic>, <italic>Boletus</italic>, <italic>Laccaria</italic>, and <italic>Tricholoma</italic> revealed the ability to utilize starch as a growth substrate (<xref ref-type="bibr" rid="B45">Ohta, 1997</xref>; <xref ref-type="bibr" rid="B31">Kusuda et al., 2006</xref>). <italic>Tuber maculatum</italic> mycelium utilized xylan as energy source during the growth cycle (<xref ref-type="bibr" rid="B2">Bedade et al., 2017</xref>). Both DNA replication and proteasome were enriched in P and F stages in <italic>P. portentosus</italic>, which were detected to be associated with development and maturation in other mushrooms (<xref ref-type="bibr" rid="B42">Masato et al., 2010</xref>; <xref ref-type="bibr" rid="B53">Rodenburg et al., 2018</xref>; <xref ref-type="bibr" rid="B61">Song et al., 2018</xref>; <xref ref-type="bibr" rid="B69">Wang et al., 2018</xref>). DNA replication is important for premeiotic replication, karyogamy, and meiosis during maturation in mushrooms, e.g., <italic>L. edodes</italic> (<xref ref-type="bibr" rid="B61">Song et al., 2018</xref>; <xref ref-type="bibr" rid="B69">Wang et al., 2018</xref>) and <italic>Botrytis cinerea</italic> (<xref ref-type="bibr" rid="B53">Rodenburg et al., 2018</xref>). The proteasome is presumably linked with fruiting body development in basidiomycetes by degrading unnecessary proteins through the ubiquitin-proteasome pathway (<xref ref-type="bibr" rid="B42">Masato et al., 2010</xref>). Furthermore, peroxisome, ribosome, oxidative phosphorylation, citrate cycle and MAPK signaling pathways were enriched in the stage of F in <italic>P. portentosus.</italic> Ribosome pathways were increased significantly during the fruiting body growth stage in <italic>Ophiocordyceps sinensis</italic> (<xref ref-type="bibr" rid="B77">Zhang et al., 2021</xref>), <italic>F. velutipes</italic> (<xref ref-type="bibr" rid="B34">Liu et al., 2014</xref>), <italic>Auricularia polytricha</italic> (<xref ref-type="bibr" rid="B80">Zhou et al., 2014</xref>), and <italic>Agaricus blazei</italic> (<xref ref-type="bibr" rid="B38">Lu et al., 2020</xref>) to provide proteins for fruiting body formation or carry out some other functions, e.g., DNA repair, development, and cell division. In fungi, the activity of peroxisomes was required for sexual development (<xref ref-type="bibr" rid="B47">Peraza-Reyes and Berteaux-Lecellier, 2013</xref>). Oxidative phosphorylation and citrate cycle were the key metabolic pathways for the growth and development of <italic>Clavariadelphus pistillaris</italic> (<xref ref-type="bibr" rid="B63">Tang et al., 2019</xref>). Higher expression of MAPK genes involved in MAPK signaling pathways is required for fruiting in some fungi, which plays an important role in promoting sexual reproduction, regulating the polar growth of mycelia and rebuilding of the cell wall in the mature fruiting body (<xref ref-type="bibr" rid="B50">P&#x00F6;ggeler et al., 2006</xref>; <xref ref-type="bibr" rid="B78">Zhang et al., 2015</xref>; <xref ref-type="bibr" rid="B33">Li et al., 2019</xref>).</p>
</sec>
<sec sec-type="conclusion" id="S5">
<title>Conclusion</title>
<p>Our results revealed fewer cell wall-degrading enzymes encoded in the genome of <italic>P. portentosus</italic> than that observed in some saprophytic mushrooms with specific ectomycorrhizal niches. The low expression of plant cell wall-degrading genes confirmed the limited ability of <italic>P. portentosus</italic> to degrade lignocellulose. In addition, some conserved and specific pathways were enriched in the different developmental stages of <italic>P. portentosus</italic>, e.g., starch and sucrose metabolism enriched in the mycelial stage and DNA replication, proteasome and MAPK signaling pathways enriched in the fruiting body stage. The results of the present study advance our understanding of the molecular mechanisms of <italic>P. portentosus</italic> lignocellulose degradation and fruiting body development.</p>
</sec>
<sec sec-type="data-availability" id="S6">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="PRJNA743691">PRJNA743691</ext-link> (<ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SRR15039576">SRR15039576</ext-link>&#x2013;<ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SRR15039584">SRR15039584</ext-link>). <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JAHRGP000000000">JAHRGP000000000</ext-link>.</p>
</sec>
<sec id="S7">
<title>Author Contributions</title>
<p>R-HY, D-PB, K-PJ, S-ZL, and QT contributed to the conception and design of the study. J-NW, YL, S-ZL, YC, and G-YJ prepared the samples. R-HY and K-PJ performed the analysis and wrote the manuscript draft. All authors approved the final version of the manuscript.</p>
</sec>
<sec sec-type="COI-statement" id="conf1">
<title>Conflict of Interest</title>
<p>K-PJ, YC, S-ZL, and G-YJ are employed by Hongzhen Agricultural Science and Technology Co. Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec sec-type="disclaimer" id="pudiscl1">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
<back>
<sec sec-type="funding-information" id="S8">
<title>Funding</title>
<p>This work was supported by Shanghai Action Plan for Scientific and Technological Innovation (19391901400) and the National Natural Science Foundation of China (32072644).</p>
</sec>
<sec id="S9" sec-type="supplementary material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fmicb.2021.732458/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fmicb.2021.732458/full#supplementary-material</ext-link></p>
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<ref-list>
<title>References</title>
<ref id="B1"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Baldrian</surname> <given-names>P.</given-names></name> <name><surname>Val&#x00E1;kov&#x00E1;</surname> <given-names>V.</given-names></name></person-group> (<year>2008</year>). <article-title>Degradation of cellulose by basidiomycetous fungi.</article-title> <source><italic>FEMS Microbiol. Rev.</italic></source> <volume>32</volume> <fpage>501</fpage>&#x2013;<lpage>521</lpage>.</citation></ref>
<ref id="B2"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bedade</surname> <given-names>D.</given-names></name> <name><surname>Berezina</surname> <given-names>O.</given-names></name> <name><surname>Singhal</surname> <given-names>R.</given-names></name> <name><surname>Deska</surname> <given-names>J.</given-names></name> <name><surname>Shamekh</surname> <given-names>S.</given-names></name></person-group> (<year>2017</year>). <article-title>Extracellular xylanase production from a new xylanase producer <italic>Tuber maculatum</italic> mycelium under submerged fermentation and its characterization.</article-title> <source><italic>Biocatalysis Agric. Biotechnol.</italic></source> <volume>11</volume> <fpage>288</fpage>&#x2013;<lpage>293</lpage>.</citation></ref>
<ref id="B3"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Blanco</surname> <given-names>E.</given-names></name> <name><surname>Parra</surname> <given-names>G.</given-names></name> <name><surname>Guigo</surname> <given-names>R.</given-names></name></person-group> (<year>2002</year>). <article-title>&#x201C;Using GeneID to identify genes,&#x201D; in</article-title> <source><italic>Current Protocols in Bioinformatics</italic></source>, <role>ed.</role> <person-group person-group-type="editor"><name><surname>Baxevanis</surname> <given-names>A.</given-names></name></person-group> (<publisher-loc>New York, NY</publisher-loc>: <publisher-name>John Wiley &#x0026; Sons Inc</publisher-name>).</citation></ref>
<ref id="B4"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>B&#x00F6;deker</surname> <given-names>I. T. M.</given-names></name> <name><surname>Nygren</surname> <given-names>C. M. R.</given-names></name> <name><surname>Taylor</surname> <given-names>A. F. S.</given-names></name> <name><surname>Olson</surname> <given-names>A.</given-names></name> <name><surname>Lindahl</surname> <given-names>B. D.</given-names></name></person-group> (<year>2009</year>). <article-title>ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi.</article-title> <source><italic>ISME J.</italic></source> <volume>3</volume> <fpage>1387</fpage>&#x2013;<lpage>1395</lpage>. <pub-id pub-id-type="doi">10.1038/ismej.2009.77</pub-id> <pub-id pub-id-type="pmid">19571893</pub-id></citation></ref>
<ref id="B5"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Boeckmann</surname> <given-names>B.</given-names></name> <name><surname>Blatter</surname> <given-names>M. C.</given-names></name> <name><surname>Famiglietti</surname> <given-names>L.</given-names></name> <name><surname>Hinz</surname> <given-names>U.</given-names></name> <name><surname>Lane</surname> <given-names>L.</given-names></name> <name><surname>Roechert</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2005</year>). <article-title>Protein variety and functional diversity: swiss-prot annotation in its biological context.</article-title> <source><italic>Comptes Rendus Biol.</italic></source> <volume>328</volume> <fpage>882</fpage>&#x2013;<lpage>899</lpage>.</citation></ref>
<ref id="B6"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Burge</surname> <given-names>C. B.</given-names></name> <name><surname>Karlin</surname> <given-names>S.</given-names></name></person-group> (<year>1998</year>) <article-title>Finding the genes in genomic DNA.</article-title> <source><italic>Curr. Opin. Struct. Biol.</italic></source> <volume>8</volume>, <fpage>346</fpage>&#x2013;<lpage>354</lpage>.</citation></ref>
<ref id="B7"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cao</surname> <given-names>Y.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name> <name><surname>Yu</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>P.</given-names></name> <name><surname>Tang</surname> <given-names>X.</given-names></name> <name><surname>He</surname> <given-names>X.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Genome sequence of <italic>Phlebopus portentosus</italic> strain PP33, a cultivated Bolete.</article-title> <source><italic>Genome Announcements</italic></source> <volume>3</volume> <fpage>e326</fpage>&#x2013;<lpage>e315</lpage>.</citation></ref>
<ref id="B8"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Chang</surname> <given-names>S. T.</given-names></name> <name><surname>Li</surname> <given-names>G.</given-names></name> <name><surname>Peberdy</surname> <given-names>J. F.</given-names></name></person-group> (<year>1985</year>). <article-title>Isolation of protoplasts from edible fungi.</article-title> <source><italic>Mircen J. Appl. Microbiol. Biotechnol.</italic></source> <volume>1</volume> <fpage>185</fpage>&#x2013;<lpage>193</lpage>.</citation></ref>
<ref id="B9"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname> <given-names>L.</given-names></name> <name><surname>Gong</surname> <given-names>Y.</given-names></name> <name><surname>Cai</surname> <given-names>Y.</given-names></name> <name><surname>Wei</surname> <given-names>L.</given-names></name> <name><surname>Bian</surname> <given-names>Y.</given-names></name></person-group> (<year>2016</year>). <article-title>Genome sequence of the edible cultivated mushroom <italic>Lentinula edodes</italic> (shiitake) reveals insights into lignocellulose degradation.</article-title> <source><italic>PLoS One</italic></source> <volume>11</volume>:<issue>e0160336</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0160336</pub-id> <pub-id pub-id-type="pmid">27500531</pub-id></citation></ref>
<ref id="B10"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Clavel</surname> <given-names>J.</given-names></name> <name><surname>Lembrechts</surname> <given-names>J.</given-names></name> <name><surname>Alexander</surname> <given-names>J.</given-names></name> <name><surname>Haider</surname> <given-names>S.</given-names></name> <name><surname>Lenoir</surname> <given-names>J.</given-names></name> <name><surname>Milbau</surname> <given-names>A.</given-names></name><etal/></person-group> (<year>2021</year>). <article-title>The role of arbuscular mycorrhizal fungi in nonnative plant invasion along mountain roads.</article-title> <source><italic>New Phytol.</italic></source> <volume>230</volume> <fpage>1156</fpage>&#x2013;<lpage>1168</lpage>. <pub-id pub-id-type="doi">10.1111/nph.16954</pub-id> <pub-id pub-id-type="pmid">32984980</pub-id></citation></ref>
<ref id="B11"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Conesa</surname> <given-names>A.</given-names></name> <name><surname>Gotz</surname> <given-names>S.</given-names></name> <name><surname>Garcia-Gomez</surname> <given-names>J. M.</given-names></name> <name><surname>Terol</surname> <given-names>J.</given-names></name> <name><surname>Talon</surname> <given-names>M.</given-names></name> <name><surname>Robles</surname> <given-names>M.</given-names></name></person-group> (<year>2005</year>). <article-title>Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.</article-title> <source><italic>Bioinformatics</italic></source> <volume>21</volume> <fpage>3674</fpage>&#x2013;<lpage>3676</lpage>. <pub-id pub-id-type="doi">10.1093/bioinformatics/bti610</pub-id> <pub-id pub-id-type="pmid">16081474</pub-id></citation></ref>
<ref id="B12"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Elisashvili</surname> <given-names>V.</given-names></name> <name><surname>Kachlishvili</surname> <given-names>E.</given-names></name> <name><surname>Penninckx</surname> <given-names>M.</given-names></name></person-group> (<year>2008</year>). <article-title>Lignocellulolytic enzymes profile during growth and fruiting of <italic>Pleurotus ostreatus</italic> on wheat straw and tree leaves.</article-title> <source><italic>Acta Microbiol. Immunol. Hungarica</italic></source> <volume>55</volume> <fpage>157</fpage>&#x2013;<lpage>168</lpage>. <pub-id pub-id-type="doi">10.1556/AMicr.55.2008.2.7</pub-id> <pub-id pub-id-type="pmid">18595320</pub-id></citation></ref>
<ref id="B13"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Finn</surname> <given-names>R. D.</given-names></name> <name><surname>Mistry</surname> <given-names>J.</given-names></name> <name><surname>Tate</surname> <given-names>J.</given-names></name> <name><surname>Coggill</surname> <given-names>P.</given-names></name> <name><surname>Heger</surname> <given-names>A.</given-names></name> <name><surname>Pollington</surname> <given-names>J. E.</given-names></name><etal/></person-group> (<year>2010</year>). <article-title>Pfam protein families database.</article-title> <source><italic>Nuclc Acids Res.</italic></source> <volume>40</volume> <fpage>290</fpage>&#x2013;<lpage>301</lpage>.</citation></ref>
<ref id="B14"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Floudas</surname> <given-names>D.</given-names></name> <name><surname>Binder</surname> <given-names>M.</given-names></name> <name><surname>Riley</surname> <given-names>R.</given-names></name> <name><surname>Barry</surname> <given-names>K.</given-names></name> <name><surname>Blanchette</surname> <given-names>R. A.</given-names></name> <name><surname>Henrissat</surname> <given-names>B.</given-names></name><etal/></person-group> (<year>2012</year>). <article-title>The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.</article-title> <source><italic>Science</italic></source> <volume>336</volume> <fpage>1715</fpage>&#x2013;<lpage>1719</lpage>. <pub-id pub-id-type="doi">10.1126/science.1221748</pub-id> <pub-id pub-id-type="pmid">22745431</pub-id></citation></ref>
<ref id="B15"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Haas</surname> <given-names>B. J.</given-names></name> <name><surname>Salzberg</surname> <given-names>S. L.</given-names></name> <name><surname>Zhu</surname> <given-names>W.</given-names></name> <name><surname>Pertea</surname> <given-names>M.</given-names></name> <name><surname>Allen</surname> <given-names>J. E.</given-names></name> <name><surname>Orvis</surname> <given-names>J.</given-names></name><etal/></person-group> (<year>2008</year>). <article-title>Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.</article-title> <source><italic>Genome Biol.</italic></source> <volume>9</volume>:<issue>R7</issue>. <pub-id pub-id-type="doi">10.1186/gb-2008-9-1-r7</pub-id> <pub-id pub-id-type="pmid">18190707</pub-id></citation></ref>
<ref id="B16"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hall</surname> <given-names>I. R.</given-names></name> <name><surname>Yun</surname> <given-names>W.</given-names></name> <name><surname>Amicucci</surname> <given-names>A.</given-names></name></person-group> (<year>2003</year>). <article-title>Cultivation of edible ectomycorrhizal mushrooms.</article-title> <source><italic>Trends Biotech.</italic></source> <volume>21</volume> <fpage>433</fpage>&#x2013;<lpage>438</lpage>.</citation></ref>
<ref id="B17"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hammel</surname> <given-names>K. E.</given-names></name></person-group> (<year>1997</year>). <article-title>&#x201C;Fungal degradation of lignin,&#x201D; in</article-title> <source><italic>Driven by Nature: Plant Litter Quality and Decomposition</italic></source>, <role>eds</role> <person-group person-group-type="editor"><name><surname>Cadisch</surname> <given-names>G.</given-names></name> <name><surname>Giller</surname> <given-names>K. E.</given-names></name></person-group> (<publisher-loc>Wallingford</publisher-loc>: <publisher-name>CAB International</publisher-name>), <fpage>33</fpage>&#x2013;<lpage>45</lpage>.</citation></ref>
<ref id="B18"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hao</surname> <given-names>H.</given-names></name> <name><surname>Zhang</surname> <given-names>J.</given-names></name> <name><surname>Wang</surname> <given-names>H.</given-names></name> <name><surname>Wang</surname> <given-names>Q.</given-names></name> <name><surname>Chen</surname> <given-names>H.</given-names></name></person-group> (<year>2019</year>). <article-title>Comparative transcriptome analysis reveals potential fruiting body formation mechanisms in <italic>Morchella importuna</italic>.</article-title> <source><italic>AMB Express</italic></source> <volume>9</volume>:<issue>103</issue>. <pub-id pub-id-type="doi">10.1186/s13568-019-0831-4</pub-id> <pub-id pub-id-type="pmid">31300949</pub-id></citation></ref>
<ref id="B19"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname> <given-names>L.</given-names></name> <name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Wu</surname> <given-names>P.</given-names></name> <name><surname>Sarah</surname> <given-names>E.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Tanner</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>46</volume> <fpage>D516</fpage>&#x2013;<lpage>D521</lpage>.</citation></ref>
<ref id="B20"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ian</surname> <given-names>K.</given-names></name></person-group> (<year>2004</year>). <article-title>Gene finding in novel genomes.</article-title> <source><italic>BMC Bioinform.</italic></source> <volume>5</volume>:<issue>59</issue>. <pub-id pub-id-type="doi">10.1186/1471-2105-5-59</pub-id> <pub-id pub-id-type="pmid">15144565</pub-id></citation></ref>
<ref id="B21"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Isikhuemhen</surname> <given-names>O. S.</given-names></name> <name><surname>Mikiashvilli</surname> <given-names>N. A.</given-names></name></person-group> (<year>2009</year>). <article-title>Lignocellulolytic enzyme activity, substrate utilization, and mushroom yield by <italic>Pleurotus ostreatus</italic> cultivated on substrate containing anaerobic digester solids.</article-title> <source><italic>J. Industrial Microbiol.</italic></source> <volume>36</volume> <fpage>1353</fpage>&#x2013;<lpage>1362</lpage>. <pub-id pub-id-type="doi">10.1007/s10295-009-0620-1</pub-id> <pub-id pub-id-type="pmid">19618225</pub-id></citation></ref>
<ref id="B22"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jaqueline</surname> <given-names>H.</given-names></name> <name><surname>Inger</surname> <given-names>S.</given-names></name> <name><surname>Maryam</surname> <given-names>C. D. M.</given-names></name> <name><surname>Matthieu</surname> <given-names>H.</given-names></name> <name><surname>Bernard</surname> <given-names>H.</given-names></name> <name><surname>Anne</surname> <given-names>P.</given-names></name></person-group> (<year>2018</year>). <article-title>Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus <italic>Amanita</italic>.</article-title> <source><italic>Mol. Biol. Evol.</italic></source> <volume>35</volume> <fpage>2786</fpage>&#x2013;<lpage>2804</lpage>. <pub-id pub-id-type="doi">10.1093/molbev/msy179</pub-id> <pub-id pub-id-type="pmid">30239843</pub-id></citation></ref>
<ref id="B23"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jens</surname> <given-names>K.</given-names></name> <name><surname>Frank</surname> <given-names>H.</given-names></name> <name><surname>Jan</surname> <given-names>G.</given-names></name></person-group> (<year>2019</year>). <article-title>GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-Seq data.</article-title> <source><italic>Methods Mol. Biol</italic>.</source> <volume>1962</volume> <fpage>161</fpage>&#x2013;<lpage>177</lpage>.</citation></ref>
<ref id="B24"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ji</surname> <given-names>K. P.</given-names></name> <name><surname>Cao</surname> <given-names>Y.</given-names></name> <name><surname>Zhang</surname> <given-names>C. X.</given-names></name> <name><surname>He</surname> <given-names>M. X.</given-names></name> <name><surname>Liu</surname> <given-names>J.</given-names></name> <name><surname>Wang</surname> <given-names>W. B.</given-names></name><etal/></person-group> (<year>2011</year>). <article-title>Cultivation of <italic>Phlebopus portentosus</italic> in southern China.</article-title> <source><italic>Mycol. Progr.</italic></source> <volume>10</volume> <fpage>293</fpage>&#x2013;<lpage>300</lpage>.</citation></ref>
<ref id="B25"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>D.</given-names></name> <name><surname>Paggi</surname> <given-names>J. M.</given-names></name> <name><surname>Park</surname> <given-names>C.</given-names></name> <name><surname>Bennett</surname> <given-names>C.</given-names></name> <name><surname>Salzberg</surname> <given-names>S. L.</given-names></name></person-group> (<year>2019</year>). <article-title>Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.</article-title> <source><italic>Nat. Biotechnol.</italic></source> <volume>37</volume>:<issue>1</issue>. <pub-id pub-id-type="doi">10.1038/s41587-019-0201-4</pub-id> <pub-id pub-id-type="pmid">31375807</pub-id></citation></ref>
<ref id="B26"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Klopfenstein</surname> <given-names>D. V.</given-names></name> <name><surname>Zhang</surname> <given-names>L.</given-names></name> <name><surname>Pedersen</surname> <given-names>B. S.</given-names></name> <name><surname>Fidel</surname> <given-names>R.</given-names></name> <name><surname>Alex</surname> <given-names>W. V.</given-names></name> <name><surname>Aur&#x00E9;lien</surname> <given-names>N.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>GOATOOLS: a python library for gene ontology analyses.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>8</volume>:<issue>10872</issue>. <pub-id pub-id-type="doi">10.1038/s41598-018-28948-z</pub-id> <pub-id pub-id-type="pmid">30022098</pub-id></citation></ref>
<ref id="B27"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kohler</surname> <given-names>A.</given-names></name> <name><surname>Kuo</surname> <given-names>A.</given-names></name> <name><surname>Nagy</surname> <given-names>L. G.</given-names></name> <name><surname>Morin</surname> <given-names>E.</given-names></name> <name><surname>Barry</surname> <given-names>K. W.</given-names></name> <name><surname>Buscot</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.</article-title> <source><italic>Nat. Genet.</italic></source> <volume>47</volume> <fpage>410</fpage>&#x2013;<lpage>415</lpage>. <pub-id pub-id-type="doi">10.1038/ng.3223</pub-id> <pub-id pub-id-type="pmid">25706625</pub-id></citation></ref>
<ref id="B28"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kumla</surname> <given-names>J.</given-names></name> <name><surname>Danell</surname> <given-names>E.</given-names></name> <name><surname>Lumyong</surname> <given-names>S.</given-names></name></person-group> (<year>2015</year>). <article-title>Improvement of yield for a tropical black bolete, <italic>Phlebopus portentosus</italic>, cultivation in northern Thailand.</article-title> <source><italic>Mycoscience</italic></source> <volume>56</volume> <fpage>114</fpage>&#x2013;<lpage>117</lpage>.</citation></ref>
<ref id="B29"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kumla</surname> <given-names>J.</given-names></name> <name><surname>Hobbie</surname> <given-names>E. A.</given-names></name> <name><surname>Suwannarach</surname> <given-names>N.</given-names></name> <name><surname>Lumyong</surname> <given-names>S.</given-names></name></person-group> (<year>2016</year>). <article-title>The ectomycorrhizal status of a tropical black bolete, <italic>Phlebopus portentosus</italic>, assessed using mycorrhizal synthesis and isotopic analysis.</article-title> <source>. <italic>Mycorrhiza</italic></source> <volume>26</volume> <fpage>333</fpage>&#x2013;<lpage>343</lpage>. <pub-id pub-id-type="doi">10.1007/s00572-015-0672-1</pub-id> <pub-id pub-id-type="pmid">26671421</pub-id></citation></ref>
<ref id="B30"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kumla</surname> <given-names>J.</given-names></name> <name><surname>Suwannarach</surname> <given-names>N.</given-names></name> <name><surname>Tanruean</surname> <given-names>K.</given-names></name> <name><surname>Lumyong</surname> <given-names>S.</given-names></name></person-group> (<year>2021</year>). <article-title>Comparative evaluation of chemical composition, phenolic compounds, and antioxidant and antimicrobial activities of tropical black bolete mushroom using different preservation methods.</article-title> <source><italic>Foods</italic></source> <volume>10</volume>:<issue>781</issue>. <pub-id pub-id-type="doi">10.3390/foods10040781</pub-id> <pub-id pub-id-type="pmid">33916446</pub-id></citation></ref>
<ref id="B31"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kusuda</surname> <given-names>M.</given-names></name> <name><surname>Ueda</surname> <given-names>M.</given-names></name> <name><surname>Konishi</surname> <given-names>Y.</given-names></name> <name><surname>Araki</surname> <given-names>Y.</given-names></name> <name><surname>Yamanaka</surname> <given-names>K.</given-names></name> <name><surname>Nakazawa</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2006</year>). <article-title>Detection of &#x03B2;-glucosidase as a saprotrophic ability from an ectomycorrhizal mushroom, <italic>Tricholoma matsutake</italic>.</article-title> <source><italic>Mycoscience</italic></source> <volume>47</volume> <fpage>184</fpage>&#x2013;<lpage>189</lpage>.</citation></ref>
<ref id="B32"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lechner</surname> <given-names>B. E.</given-names></name> <name><surname>Papinutti</surname> <given-names>V. L.</given-names></name></person-group> (<year>2006</year>). <article-title>Production of lignocellulosic enzymes during growth and fruiting of the edible fungus <italic>Lentinus tigrinus</italic> on wheat straw.</article-title> <source><italic>Process Biochem.</italic></source> <volume>41</volume> <fpage>594</fpage>&#x2013;<lpage>598</lpage>.</citation></ref>
<ref id="B33"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Wang</surname> <given-names>F.</given-names></name> <name><surname>Liu</surname> <given-names>Q.</given-names></name> <name><surname>Li</surname> <given-names>Q.</given-names></name> <name><surname>Qian</surname> <given-names>Z.</given-names></name> <name><surname>Zhang</surname> <given-names>X.</given-names></name><etal/></person-group> (<year>2019</year>). <article-title>Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes.</article-title> <source><italic>BMC Genomics</italic></source> <volume>20</volume>:<issue>337</issue>. <pub-id pub-id-type="doi">10.1186/s12864-019-5708-z</pub-id> <pub-id pub-id-type="pmid">31054562</pub-id></citation></ref>
<ref id="B34"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>F.</given-names></name> <name><surname>Wang</surname> <given-names>W.</given-names></name> <name><surname>Xie</surname> <given-names>B.</given-names></name></person-group> (<year>2014</year>). <article-title>Comparison of gene expression patterns in the mycelium and primordia of Flammulina velutipes, strain 1123.</article-title> <source><italic>Acta Edulis Fungi</italic></source> <volume>21</volume> <fpage>1</fpage>&#x2013;<lpage>7</lpage>.</citation></ref>
<ref id="B35"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>X. B.</given-names></name> <name><surname>Orcid</surname> <given-names>I.</given-names></name> <name><surname>Xia</surname> <given-names>E. H.</given-names></name> <name><surname>Li</surname> <given-names>M.</given-names></name> <name><surname>Cui</surname> <given-names>Y. Y.</given-names></name> <name><surname>Wang</surname> <given-names>P. M.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Transcriptome data reveal conserved patterns of fruiting body development and response to heat stress in the mushroom-forming fungus <italic>Flammulina filiformis</italic>.</article-title> <source><italic>PLoS One</italic></source> <volume>15</volume>:<issue>e0239890</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0239890</pub-id> <pub-id pub-id-type="pmid">33064719</pub-id></citation></ref>
<ref id="B36"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Love</surname> <given-names>M. I</given-names></name> <name><surname>Huber</surname> <given-names>W.</given-names></name> <name><surname>Anders</surname> <given-names>S.</given-names></name></person-group> (<year>2014</year>). <article-title>Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.</article-title> <source><italic>Genome Biol.</italic></source> <volume>15</volume>:<issue>550</issue>. <pub-id pub-id-type="doi">10.1186/s13059-014-0550-8</pub-id> <pub-id pub-id-type="pmid">25516281</pub-id></citation></ref>
<ref id="B37"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lowe</surname> <given-names>T. M.</given-names></name> <name><surname>Eddy</surname> <given-names>S. R.</given-names></name></person-group> (<year>1997</year>). <article-title>tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>25</volume> <fpage>955</fpage>&#x2013;<lpage>964</lpage>. <pub-id pub-id-type="doi">10.1093/nar/25.5.955</pub-id> <pub-id pub-id-type="pmid">9023104</pub-id></citation></ref>
<ref id="B38"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lu</surname> <given-names>Y. P.</given-names></name> <name><surname>Liao</surname> <given-names>J. H.</given-names></name> <name><surname>Guo</surname> <given-names>Z. J.</given-names></name> <name><surname>Cai</surname> <given-names>Z. X.</given-names></name> <name><surname>Chen</surname> <given-names>M. Y.</given-names></name></person-group> (<year>2020</year>). <article-title>Genome survey and transcriptome analysis on mycelia and primordia of <italic>Agaricus blazei</italic>.</article-title> <source><italic>BioMed. Res. Int.</italic></source> <volume>11</volume> <fpage>1</fpage>&#x2013;<lpage>12</lpage>. <pub-id pub-id-type="doi">10.1155/2020/1824183</pub-id> <pub-id pub-id-type="pmid">32025516</pub-id></citation></ref>
<ref id="B39"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Majoros</surname> <given-names>W.</given-names></name> <name><surname>Pertea</surname> <given-names>M.</given-names></name> <name><surname>Salzberg</surname> <given-names>S.</given-names></name></person-group> (<year>2004</year>). <article-title>TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.</article-title> <source><italic>Bioinformatics</italic></source> <volume>20</volume> <fpage>2878</fpage>&#x2013;<lpage>2879</lpage>. <pub-id pub-id-type="doi">10.1093/bioinformatics/bth315</pub-id> <pub-id pub-id-type="pmid">15145805</pub-id></citation></ref>
<ref id="B40"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mario</surname> <given-names>S.</given-names></name> <name><surname>Burkhard</surname> <given-names>M.</given-names></name></person-group> (<year>2005</year>). <article-title>AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>33</volume> <fpage>465</fpage>&#x2013;<lpage>467</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gki458</pub-id> <pub-id pub-id-type="pmid">15980513</pub-id></citation></ref>
<ref id="B41"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Martin</surname> <given-names>F.</given-names></name> <name><surname>Kohler</surname> <given-names>A.</given-names></name> <name><surname>Murat</surname> <given-names>C.</given-names></name> <name><surname>Veneault-Fourrey</surname> <given-names>C.</given-names></name> <name><surname>Hibbett</surname> <given-names>D. S.</given-names></name></person-group> (<year>2016</year>). <article-title>Unearthing the roots of ectomycorrhizal symbioses.</article-title> <source><italic>Nat. Rev. Microbiol.</italic></source> <volume>14</volume> <fpage>760</fpage>&#x2013;<lpage>773</lpage>. <pub-id pub-id-type="doi">10.1038/nrmicro.2016.149</pub-id> <pub-id pub-id-type="pmid">27795567</pub-id></citation></ref>
<ref id="B42"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Masato</surname> <given-names>Y.</given-names></name> <name><surname>Sou</surname> <given-names>S.</given-names></name> <name><surname>Kou</surname> <given-names>S.</given-names></name> <name><surname>Goro</surname> <given-names>T.</given-names></name> <name><surname>Satoshi</surname> <given-names>I.</given-names></name> <name><surname>Mitsuo</surname> <given-names>O.</given-names></name><etal/></person-group> (<year>2010</year>). <article-title>Isolation and analysis of genes specifically expressed during fruiting body development in the basidiomycete <italic>Flammulina velutipes</italic> by fluorescence differential display.</article-title> <source><italic>FEMS Microbiol. Lett.</italic></source> <volume>254</volume> <fpage>165</fpage>&#x2013;<lpage>172</lpage>. <pub-id pub-id-type="doi">10.1111/j.1574-6968.2005.00023.x</pub-id> <pub-id pub-id-type="pmid">16451195</pub-id></citation></ref>
<ref id="B43"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Miyauchi</surname> <given-names>S.</given-names></name> <name><surname>Kiss</surname> <given-names>E.</given-names></name> <name><surname>Kuo</surname> <given-names>A.</given-names></name> <name><surname>Drula</surname> <given-names>E.</given-names></name> <name><surname>Kohler</surname> <given-names>A.</given-names></name> <name><surname>S&#x00E1;nchez-Garc&#x00ED;a</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2020</year>). <article-title>Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.</article-title> <source><italic>Nat. Commun.</italic></source> <volume>11</volume>:<issue>5125</issue>. <pub-id pub-id-type="doi">10.1038/s41467-020-18795-w</pub-id> <pub-id pub-id-type="pmid">33046698</pub-id></citation></ref>
<ref id="B44"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Nawrocki</surname> <given-names>E. P.</given-names></name></person-group> (<year>2014</year>). <article-title>Annotating functional RNAs in genomes using Infernal.</article-title> <source><italic>Methods Mol. Biol.</italic></source> <volume>1097</volume> <fpage>163</fpage>&#x2013;<lpage>197</lpage>.</citation></ref>
<ref id="B45"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ohta</surname> <given-names>A.</given-names></name></person-group> (<year>1997</year>). <article-title>Ability of ectomycorrhizal fungi to utilize starch and related substrates.</article-title> <source><italic>Mycoscience</italic></source> <volume>38</volume> <fpage>403</fpage>&#x2013;<lpage>408</lpage>.</citation></ref>
<ref id="B46"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Oksanen</surname> <given-names>J.</given-names></name> <name><surname>Blanchet</surname> <given-names>F. G.</given-names></name> <name><surname>Kindt</surname> <given-names>R.</given-names></name> <name><surname>Legendre</surname> <given-names>P.</given-names></name> <name><surname>O&#x2019;Hara</surname> <given-names>R. B.</given-names></name></person-group> (<year>2011</year>). <source><italic>R package.</italic></source></citation></ref>
<ref id="B47"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Peraza-Reyes</surname> <given-names>L.</given-names></name> <name><surname>Berteaux-Lecellier</surname> <given-names>V.</given-names></name></person-group> (<year>2013</year>). <article-title>Peroxisomes and sexual development in fungi.</article-title> <source><italic>Front. Physiol.</italic></source> <volume>4</volume>:<issue>244</issue>. <pub-id pub-id-type="doi">10.3389/fphys.2013.00244</pub-id> <pub-id pub-id-type="pmid">24046747</pub-id></citation></ref>
<ref id="B48"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pertea</surname> <given-names>M.</given-names></name> <name><surname>Pertea</surname> <given-names>G. M.</given-names></name> <name><surname>Antonescu</surname> <given-names>C. M.</given-names></name> <name><surname>Chang</surname> <given-names>T. C.</given-names></name> <name><surname>Mendell</surname> <given-names>J. T.</given-names></name> <name><surname>Salzberg</surname> <given-names>S. L.</given-names></name></person-group> (<year>2015</year>). <article-title>StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.</article-title> <source><italic>Nat. Biotechnol.</italic></source> <volume>33</volume> <fpage>290</fpage>&#x2013;<lpage>295</lpage>. <pub-id pub-id-type="doi">10.1038/nbt.3122</pub-id> <pub-id pub-id-type="pmid">25690850</pub-id></citation></ref>
<ref id="B49"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pham</surname> <given-names>N.</given-names></name> <name><surname>Yamada</surname> <given-names>A.</given-names></name> <name><surname>Shimizu</surname> <given-names>K.</given-names></name> <name><surname>Noda</surname> <given-names>K.</given-names></name> <name><surname>Dang</surname> <given-names>L.</given-names></name> <name><surname>Suzuki</surname> <given-names>A.</given-names></name></person-group> (<year>2012</year>). <article-title>A sheathing mycorrhiza between the tropical bolete <italic>Phlebopus spongiosus</italic> and <italic>Citrus maxima</italic>.</article-title> <source><italic>Mycoscience</italic></source> <volume>53</volume> <fpage>347</fpage>&#x2013;<lpage>353</lpage>.</citation></ref>
<ref id="B50"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>P&#x00F6;ggeler</surname> <given-names>S.</given-names></name> <name><surname>Nowrousian</surname> <given-names>M.</given-names></name> <name><surname>Ringelberg</surname> <given-names>C.</given-names></name> <name><surname>Loros</surname> <given-names>J. J.</given-names></name> <name><surname>Dunlap</surname> <given-names>J. C.</given-names></name> <name><surname>K&#x00FC;ck</surname> <given-names>U.</given-names></name></person-group> (<year>2006</year>). <article-title>Microarray and real-time PCR analyses reveal mating type-dependent gene expression in a homothallic fungus.</article-title> <source><italic>Mol. Genet. Genomics</italic></source> <volume>275</volume> <fpage>492</fpage>&#x2013;<lpage>503</lpage>. <pub-id pub-id-type="doi">10.1007/s00438-006-0107-y</pub-id> <pub-id pub-id-type="pmid">16482473</pub-id></citation></ref>
<ref id="B51"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Quevillon</surname> <given-names>E.</given-names></name> <name><surname>Silventoinen</surname> <given-names>V.</given-names></name> <name><surname>Pillai</surname> <given-names>S.</given-names></name> <name><surname>Harte</surname> <given-names>N.</given-names></name> <name><surname>Mulder</surname> <given-names>N.</given-names></name> <name><surname>Apweiler</surname> <given-names>R.</given-names></name><etal/></person-group> (<year>2005</year>). <article-title>InterProScan: protein domains identifier.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>33</volume> <fpage>W116</fpage>&#x2013;<lpage>W120</lpage>.</citation></ref>
<ref id="B52"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>R&#x00E9;dei</surname> <given-names>G.</given-names></name></person-group> (<year>2008</year>). <source><italic>TREMBL. Encyclopedia of Genetics, Genomics, Proteomics and Informatics.</italic></source> <publisher-loc>Berlin</publisher-loc>: <publisher-name>Springer</publisher-name>.</citation></ref>
<ref id="B53"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Rodenburg</surname> <given-names>S.</given-names></name> <name><surname>Terhem</surname> <given-names>R. B.</given-names></name> <name><surname>Veloso</surname> <given-names>J.</given-names></name> <name><surname>Stassen</surname> <given-names>J.</given-names></name> <name><surname>Kan</surname> <given-names>J. V.</given-names></name> <name><surname>Turgeon</surname> <given-names>B. G.</given-names></name></person-group> (<year>2018</year>). <article-title>Functional analysis of mating type genes and transcriptome analysis during fruiting body development of <italic>Botrytis cinerea</italic>.</article-title> <source><italic>Mbio</italic></source> <volume>9</volume> <fpage>e1939</fpage>&#x2013;<lpage>e1917</lpage>. <pub-id pub-id-type="doi">10.1128/mBio.01939-17</pub-id> <pub-id pub-id-type="pmid">29440571</pub-id></citation></ref>
<ref id="B54"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ruan</surname> <given-names>J.</given-names></name> <name><surname>Li</surname> <given-names>H.</given-names></name></person-group> (<year>2020</year>). <article-title>Fast and accurate long-read assembly with wtdbg2.</article-title> <source><italic>Nat. Methods</italic></source> <volume>17</volume> <fpage>1</fpage>&#x2013;<lpage>4</lpage>. <pub-id pub-id-type="doi">10.1038/s41592-019-0669-3</pub-id> <pub-id pub-id-type="pmid">31819265</pub-id></citation></ref>
<ref id="B55"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sahoo</surname> <given-names>N.</given-names></name></person-group> (<year>2017</year>). <source><italic>Sequence Base-Calling Through Albacore Software: A Part of the Oxford Nanopore Technology.</italic></source> <comment>MSc thesis.</comment> <publisher-loc>Odisha</publisher-loc>: <publisher-name>Orissa University of Agriculture and Technology, Bhubaneswar, India</publisher-name>. <volume>Vol. 27</volume> <fpage>722</fpage>&#x2013;<lpage>736</lpage>.</citation></ref>
<ref id="B56"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sanmee</surname> <given-names>R.</given-names></name> <name><surname>Lumyong</surname> <given-names>P.</given-names></name> <name><surname>Dell</surname> <given-names>B.</given-names></name> <name><surname>Lumyong</surname> <given-names>S.</given-names></name></person-group> (<year>2010</year>). <article-title>In vitro cultivation and fruit body formation of the black bolete, <italic>Phlebopus portentosus</italic>, a popular edible ectomycorrhizal fungus in Thailand.</article-title> <source><italic>Mycoence</italic></source> <volume>51</volume> <fpage>15</fpage>&#x2013;<lpage>22</lpage>.</citation></ref>
<ref id="B57"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sergey</surname> <given-names>K.</given-names></name> <name><surname>Brian</surname> <given-names>P.</given-names></name> <name><surname>Konstantin</surname> <given-names>B.</given-names></name></person-group> (<year>2017</year>). <article-title>Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.</article-title> <source><italic>Genome Research</italic></source> <volume>27</volume> <fpage>722</fpage>&#x2013;<lpage>736</lpage>. <pub-id pub-id-type="doi">10.1101/gr.215087.116</pub-id> <pub-id pub-id-type="pmid">28298431</pub-id></citation></ref>
<ref id="B58"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shah</surname> <given-names>F.</given-names></name> <name><surname>Nicol&#x00E1;s</surname> <given-names>C.</given-names></name> <name><surname>Bentzer</surname> <given-names>J.</given-names></name> <name><surname>Ellstr&#x00F6;m</surname> <given-names>M.</given-names></name> <name><surname>Smits</surname> <given-names>M.</given-names></name> <name><surname>Rineau</surname> <given-names>F.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.</article-title> <source><italic>N. Phytol.</italic></source> <volume>209</volume> <fpage>1705</fpage>&#x2013;<lpage>1719</lpage>. <pub-id pub-id-type="doi">10.1111/nph.13722</pub-id> <pub-id pub-id-type="pmid">26527297</pub-id></citation></ref>
<ref id="B59"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shoji</surname> <given-names>O.</given-names></name> <name><surname>Royse</surname> <given-names>D. J.</given-names></name></person-group> (<year>2001</year>). <article-title>Transcriptional regulation of laccase and cellulase genes during growth and fruiting of <italic>Lentinula edodes</italic> on supplemented sawdust.</article-title> <source><italic>FEMS Microbiol. Lett.</italic></source> <volume>201</volume> <fpage>111</fpage>&#x2013;<lpage>115</lpage>. <pub-id pub-id-type="doi">10.1111/j.1574-6968.2001.tb10741.x</pub-id> <pub-id pub-id-type="pmid">11445176</pub-id></citation></ref>
<ref id="B60"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sim&#x00E3;o</surname> <given-names>F.</given-names></name> <name><surname>Waterhouse</surname> <given-names>R. M.</given-names></name> <name><surname>Panagiotis</surname> <given-names>I.</given-names></name> <name><surname>Kriventseva</surname> <given-names>E. V.</given-names></name> <name><surname>Zdobnov</surname> <given-names>E. M.</given-names></name></person-group> (<year>2015</year>). <article-title>BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.</article-title> <source><italic>Bioinformatics</italic></source> <volume>31</volume> <fpage>3210</fpage>&#x2013;<lpage> 3212</lpage>.</citation></ref>
<ref id="B61"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Song</surname> <given-names>H. Y.</given-names></name> <name><surname>Dae-Hyuk</surname> <given-names>K.</given-names></name> <name><surname>Jung-Mi</surname> <given-names>K.</given-names></name></person-group> (<year>2018</year>). <article-title>Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom <italic>Lentinula edodes</italic>.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>8</volume>:<issue>8983</issue>. <pub-id pub-id-type="doi">10.1038/s41598-018-27318-z</pub-id> <pub-id pub-id-type="pmid">29895888</pub-id></citation></ref>
<ref id="B62"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sun</surname> <given-names>Z.</given-names></name> <name><surname>Hu</surname> <given-names>M.</given-names></name> <name><surname>Sun</surname> <given-names>Z.</given-names></name> <name><surname>Zhu</surname> <given-names>N.</given-names></name> <name><surname>Yang</surname> <given-names>J.</given-names></name> <name><surname>Ma</surname> <given-names>G.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Pyrrole alkaloids from the edible mushroom Phlebopus portentosus with their bioactive activities.</article-title> <source><italic>Molecules</italic></source> <volume>23</volume>:<issue>1198</issue>. <pub-id pub-id-type="doi">10.3390/molecules23051198</pub-id> <pub-id pub-id-type="pmid">29772776</pub-id></citation></ref>
<ref id="B63"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tang</surname> <given-names>X.</given-names></name> <name><surname>Ding</surname> <given-names>X.</given-names></name> <name><surname>Dong</surname> <given-names>M.</given-names></name> <name><surname>Zhu</surname> <given-names>M.</given-names></name> <name><surname>Song</surname> <given-names>Z.</given-names></name> <name><surname>Hou</surname> <given-names>Y.</given-names></name></person-group> (<year>2019</year>). <article-title>Transcriptome analysis of Clavariadelphus pistillaris fruiting bodies atdifferent development stages.</article-title> <source><italic>Biotechnol. Bull.</italic></source> <volume>35</volume> <fpage>119</fpage>&#x2013;<lpage>129</lpage>.</citation></ref>
<ref id="B64"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tang</surname> <given-names>X.</given-names></name> <name><surname>Ding</surname> <given-names>X.</given-names></name> <name><surname>Hou</surname> <given-names>Y. L.</given-names></name></person-group> (<year>2020</year>). <article-title>Comparative analysis of transcriptomes revealed the molecular mechanism of development of <italic>Tricholoma matsutake</italic> at different stages of fruiting bodies.</article-title> <source><italic>Food Sci. Biotechnol.</italic></source> <volume>29</volume> <fpage>939</fpage>&#x2013;<lpage>951</lpage>. <pub-id pub-id-type="doi">10.1007/s10068-020-00732-8</pub-id> <pub-id pub-id-type="pmid">32582456</pub-id></citation></ref>
<ref id="B65"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tseng</surname> <given-names>M. C.</given-names></name> <name><surname>Luong</surname> <given-names>J. H.</given-names></name></person-group> (<year>1984</year>). <article-title>Mushroom cultivation - technology for commercial production.</article-title> <source><italic>Annu. Rep. Fermentation Processes</italic></source> <volume>7</volume> <fpage>45</fpage>&#x2013;<lpage>79</lpage>.</citation></ref>
<ref id="B66"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Vel&#x00E1;zquez-Cede&#x00F1;o</surname> <given-names>M.</given-names></name> <name><surname>Mata</surname> <given-names>G.</given-names></name> <name><surname>Savoie</surname> <given-names>J. M.</given-names></name></person-group> (<year>2002</year>). <article-title>Waste-reducing cultivation of Pleurotus ostreatus and <italic>Pleurotus pulmonarius</italic> on coffee pulp: changes in the production of some lignocellulolytic enzymes.</article-title> <source><italic>World J. Microbiol. Biotechnol.</italic></source> <volume>18</volume> <fpage>201</fpage>&#x2013;<lpage>207</lpage>.</citation></ref>
<ref id="B67"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Walker</surname> <given-names>B. J.</given-names></name> <name><surname>Abeel</surname> <given-names>T.</given-names></name> <name><surname>Shea</surname> <given-names>T.</given-names></name> <name><surname>Priest</surname> <given-names>M.</given-names></name> <name><surname>Earl</surname> <given-names>A. M.</given-names></name></person-group> (<year>2014</year>). <article-title>Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.</article-title> <source><italic>PLoS One</italic></source> <volume>9</volume>:<issue>e112963</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0112963</pub-id> <pub-id pub-id-type="pmid">25409509</pub-id></citation></ref>
<ref id="B68"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>M.</given-names></name> <name><surname>Gu</surname> <given-names>B.</given-names></name> <name><surname>Huang</surname> <given-names>J.</given-names></name> <name><surname>Jiang</surname> <given-names>S.</given-names></name> <name><surname>Chen</surname> <given-names>Y.</given-names></name> <name><surname>Yin</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2013</year>). <article-title>Transcriptome and proteome exploration to provide a resource for the study of <italic>Agrocybe aegerita</italic>.</article-title> <source><italic>PLoS One</italic></source> <volume>8</volume>:<issue>e56686</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0056686</pub-id> <pub-id pub-id-type="pmid">23418592</pub-id></citation></ref>
<ref id="B69"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>Y.</given-names></name> <name><surname>Zeng</surname> <given-names>X.</given-names></name> <name><surname>Liu</surname> <given-names>W.</given-names></name></person-group> (<year>2018</year>). <article-title>De novo transcriptomic analysis during <italic>Lentinula edodes</italic> fruiting body growth.</article-title> <source><italic>Gene</italic></source> <volume>641</volume> <fpage>326</fpage>&#x2013;<lpage>334</lpage>. <pub-id pub-id-type="doi">10.1016/j.gene.2017.10.061</pub-id> <pub-id pub-id-type="pmid">29066302</pub-id></citation></ref>
<ref id="B70"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wei</surname> <given-names>L.</given-names></name> <name><surname>Cai</surname> <given-names>Y.</given-names></name> <name><surname>He</surname> <given-names>P.</given-names></name> <name><surname>Chen</surname> <given-names>L.</given-names></name> <name><surname>Bian</surname> <given-names>Y.</given-names></name></person-group> (<year>2019</year>). <article-title>Comparative transcriptomics reveals potential genes involved in the vegetative growth of <italic>Morchella importuna</italic>.</article-title> <source><italic>3 Biotech</italic></source> <volume>9</volume>:<issue>81</issue>. <pub-id pub-id-type="doi">10.1007/s13205-019-1614-y</pub-id> <pub-id pub-id-type="pmid">30800592</pub-id></citation></ref>
<ref id="B71"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname> <given-names>B.</given-names></name> <name><surname>Xu</surname> <given-names>Z.</given-names></name> <name><surname>Knudson</surname> <given-names>A.</given-names></name> <name><surname>Carlson</surname> <given-names>A.</given-names></name> <name><surname>Chen</surname> <given-names>N.</given-names></name> <name><surname>Kovaka</surname> <given-names>S.</given-names></name><etal/></person-group> (<year>2018</year>). <article-title>Genomics and development of <italic>Lentinus tigrinus</italic>: a white-rot wood-decaying mushroom with dimorphic fruiting bodies.</article-title> <source><italic>Genome Biol. Evol.</italic></source> <volume>10</volume> <fpage>3250</fpage>&#x2013;<lpage>3261</lpage>. <pub-id pub-id-type="doi">10.1093/gbe/evy246</pub-id> <pub-id pub-id-type="pmid">30398645</pub-id></citation></ref>
<ref id="B72"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Xie</surname> <given-names>C.</given-names></name> <name><surname>Gong</surname> <given-names>W.</given-names></name> <name><surname>Zhu</surname> <given-names>Z.</given-names></name> <name><surname>Yan</surname> <given-names>L.</given-names></name> <name><surname>Hu</surname> <given-names>Z.</given-names></name> <name><surname>Peng</surname> <given-names>Y.</given-names></name></person-group> (<year>2018</year>). <article-title>Comparative transcriptomics of <italic>Pleurotus eryngii</italic> reveals blue-light regulation of carbohydrate-active enzymes (CAZymes) expression at primordium differentiated into fruiting body stage.</article-title> <source><italic>Genomics</italic></source> <volume>110</volume> <fpage>201</fpage>&#x2013;<lpage>209</lpage>. <pub-id pub-id-type="doi">10.1016/j.ygeno.2017.09.012</pub-id> <pub-id pub-id-type="pmid">28970048</pub-id></citation></ref>
<ref id="B73"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname> <given-names>R. H.</given-names></name> <name><surname>Bao</surname> <given-names>D. P.</given-names></name> <name><surname>Guo</surname> <given-names>T.</given-names></name> <name><surname>Li</surname> <given-names>Y.</given-names></name> <name><surname>Tan</surname> <given-names>Q.</given-names></name></person-group> (<year>2019</year>). <article-title>Bacterial profiling and dynamic succession analysis of <italic>Phlebopus portentosus</italic> casing soil using MiSeq sequencing.</article-title> <source><italic>Front. Microbiol.</italic></source> <volume>10</volume>:<issue>1927</issue>. <pub-id pub-id-type="doi">10.3389/fmicb.2019.01927</pub-id> <pub-id pub-id-type="pmid">31507552</pub-id></citation></ref>
<ref id="B74"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname> <given-names>R. H.</given-names></name> <name><surname>Li</surname> <given-names>Y.</given-names></name> <name><surname>W&#x00E1;ng</surname> <given-names>Y.</given-names></name> <name><surname>Wan</surname> <given-names>J. N.</given-names></name> <name><surname>Zhou</surname> <given-names>C. L.</given-names></name> <name><surname>W&#x00E3;ng</surname> <given-names>Y.</given-names></name><etal/></person-group> (<year>2016</year>). <article-title>The genome of Pleurotus eryngii provides insights into the mechanisms of wood decay.</article-title> <source><italic>J. Biotechnol.</italic></source> <volume>239</volume> <fpage>65</fpage>&#x2013;<lpage>67</lpage>. <pub-id pub-id-type="doi">10.1016/j.jbiotec.2016.10.007</pub-id> <pub-id pub-id-type="pmid">27737781</pub-id></citation></ref>
<ref id="B75"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yuki</surname> <given-names>M.</given-names></name> <name><surname>Masumi</surname> <given-names>I.</given-names></name> <name><surname>Shujiro</surname> <given-names>O.</given-names></name> <name><surname>Yoshizawa</surname> <given-names>A. C.</given-names></name> <name><surname>Minoru</surname> <given-names>K.</given-names></name></person-group> (<year>2007</year>). <article-title>KAAS: an automatic genome annotation and pathway reconstruction server.</article-title> <source><italic>Nucleic Acids Res.</italic></source> <volume>35</volume> <fpage>W182</fpage>&#x2013;<lpage>W185</lpage>.</citation></ref>
<ref id="B76"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>C.</given-names></name> <name><surname>He</surname> <given-names>M.</given-names></name> <name><surname>Jing</surname> <given-names>L.</given-names></name> <name><surname>Xu</surname> <given-names>X.</given-names></name> <name><surname>Yun</surname> <given-names>W.</given-names></name></person-group> (<year>2017</year>). <article-title>Brief introduction to a unique edible Bolete-<italic>Phlebopus portentosus</italic> in southern China.</article-title> <source><italic>J. Agric. Sci. Technol. B</italic></source> <volume>7</volume> <fpage>386</fpage>&#x2013;<lpage>394</lpage>.</citation></ref>
<ref id="B77"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>H.</given-names></name> <name><surname>Yue</surname> <given-names>P.</given-names></name> <name><surname>Tong</surname> <given-names>X.</given-names></name> <name><surname>Bai</surname> <given-names>J.</given-names></name> <name><surname>Guo</surname> <given-names>J.</given-names></name></person-group> (<year>2021</year>). <article-title>mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting body in ophiocordyceps sinensis.</article-title> <source><italic>Sci. Rep.</italic></source> <volume>11</volume>:<issue>12944</issue>. <pub-id pub-id-type="doi">10.1038/s41598-021-91718-x</pub-id> <pub-id pub-id-type="pmid">34155233</pub-id></citation></ref>
<ref id="B78"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>J.</given-names></name> <name><surname>Ren</surname> <given-names>A.</given-names></name> <name><surname>Chen</surname> <given-names>H.</given-names></name> <name><surname>Zhao</surname> <given-names>M.</given-names></name> <name><surname>Shi</surname> <given-names>L.</given-names></name> <name><surname>Chen</surname> <given-names>M.</given-names></name><etal/></person-group> (<year>2015</year>). <article-title>Transcriptome analysis and its application in identifying genes associated with fruiting body development in Basidiomycete <italic>Hypsizygus marmoreus</italic>.</article-title> <source><italic>PLoS One</italic></source> <volume>10</volume>:<issue>e0123025</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0123025</pub-id> <pub-id pub-id-type="pmid">25837428</pub-id></citation></ref>
<ref id="B79"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhou</surname> <given-names>S.</given-names></name> <name><surname>Zhang</surname> <given-names>J.</given-names></name> <name><surname>Ma</surname> <given-names>F.</given-names></name> <name><surname>Tang</surname> <given-names>C.</given-names></name> <name><surname>Tang</surname> <given-names>Q.</given-names></name> <name><surname>Zhang</surname> <given-names>X.</given-names></name></person-group> (<year>2018</year>). <article-title>Investigation of lignocellulolytic enzymes during different growth phases of <italic>Ganoderma lucidum</italic> strain G0119 using genomic, transcriptomic and secretomic analyses.</article-title> <source><italic>PLoS One</italic></source> <volume>13</volume>:<issue>e0198404</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0198404</pub-id> <pub-id pub-id-type="pmid">29852018</pub-id></citation></ref>
<ref id="B80"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhou</surname> <given-names>Y.</given-names></name> <name><surname>Chen</surname> <given-names>L.</given-names></name> <name><surname>Fan</surname> <given-names>X.</given-names></name> <name><surname>Bian</surname> <given-names>Y.</given-names></name> <name><surname>Michael</surname> <given-names>F.</given-names></name></person-group> (<year>2014</year>). <article-title>De novo assembly of <italic>Auricularia polytricha</italic> transcriptome using illumina sequencing for gene discovery and ssr marker identification.</article-title> <source><italic>PLoS One</italic></source> <volume>9</volume>:<issue>e91740</issue>. <pub-id pub-id-type="doi">10.1371/journal.pone.0091740</pub-id> <pub-id pub-id-type="pmid">24626227</pub-id></citation></ref>
</ref-list><fn-group>
<fn id="footnote1">
<label>1</label>
<p><ext-link ext-link-type="uri" xlink:href="http://genome.jgi.doe.gov/31_SAP">http://genome.jgi.doe.gov/31_SAP</ext-link></p></fn>
</fn-group>
</back>
</article>
