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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title>Frontiers in Plant Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Plant Sci.</abbrev-journal-title>
<issn pub-type="epub">1664-462X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fpls.2021.738880</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Plant Science</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Global Investigation of TBL Gene Family in Rose (<italic>Rosa chinensis</italic>) Unveils <italic>RcTBL16</italic> Is a Susceptibility Gene in Gray Mold Resistance</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Tian</surname>
<given-names>Yu</given-names>
</name>
<uri xlink:href="https://loop.frontiersin.org/people/1426925/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Shiya</given-names>
</name>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Xintong</given-names>
</name>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Zhang</surname>
<given-names>Zhao</given-names>
</name>
<xref rid="c001" ref-type="corresp"><sup>&#x002A;</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/441160/overview"/>
</contrib>
</contrib-group>
<aff><institution>Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University</institution>, <addr-line>Beijing</addr-line>, <country>China</country>
</aff>
<author-notes>
<fn id="fn1" fn-type="edited-by"><p>Edited by: Meixiang Zhang, Nanjing Agricultural University, China</p></fn>
<fn id="fn2" fn-type="edited-by"><p>Reviewed by: Qiong Zhang, University of California, Berkeley, United States; Biao Gu, Northwest A and F University, China</p></fn>
<corresp id="c001">&#x002A;Correspondence: Zhao Zhang, <email>zhangzhao@cau.edu.cn</email></corresp>
<fn id="fn3" fn-type="other"><p>This article was submitted to Plant Pathogen Interactions, a section of the journal Frontiers in Plant Science</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>01</day>
<month>10</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>12</volume>
<elocation-id>738880</elocation-id>
<history>
<date date-type="received">
<day>09</day>
<month>07</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>24</day>
<month>08</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2021 Tian, Zhang, Liu and Zhang.</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Tian, Zhang, Liu and Zhang</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>The TRICHOME BIREFRINGENCE-LIKE (TBL) family is an important gene family engaged in the <italic>O</italic>-acetylation of cell wall polysaccharides. There have been a few reports showing that TBL participated in the resistance against phytopathogens in Arabidopsis and rice. However, no relevant studies in rose (<italic>Rosa</italic> sp.) have been published. In this study, a genome-wide analysis of the <italic>TBL</italic> gene family in rose was presented, including their phylogenetic relationships, gene structure, chromosomal positioning, and collinearity analysis. The phylogenetic analysis revealed a total of 50 <italic>RcTBL</italic> genes in the rose genome, and they are unevenly distributed across all seven chromosomes. The occurrence of gene duplication events suggests that both the whole genome duplication and partial duplication may play a role in gene duplication of <italic>RcTBL</italic>s. The analysis of Ka/Ks showed that the replicated <italic>RcTBL</italic> genes underwent mainly purifying selection with limited functional differentiation. Gene expression analysis indicated that 12 <italic>RcTBL</italic>s were down-regulated upon the infection of <italic>Botrytis cinerea</italic>, the causal agent of the gray mold disease of rose. These <italic>RcTBL</italic>s may be a sort of candidate genes for regulating the response of rose to <italic>B. cinerea</italic>. Through virus-induced gene silencing, <italic>RcTBL16</italic> was shown to be associated with susceptibility to gray mold in rose. Through this study, meaningful information for further studies on the function of the TBL protein family in rose is provided.</p>
</abstract>
<kwd-group>
<kwd><italic>Rosa</italic> sp.</kwd>
<kwd>TBL</kwd>
<kwd><italic>Botrytis cinerea</italic></kwd>
<kwd>gene family</kwd>
<kwd>expression</kwd>
<kwd><italic>S</italic>-gene</kwd>
</kwd-group>
<contract-num rid="cn1">31772344</contract-num>
<contract-num rid="cn2">Z181100002518002</contract-num>
<contract-sponsor id="cn1">National Natural Science Foundation of China<named-content content-type="fundref-id">10.13039/501100001809</named-content>
</contract-sponsor>
<contract-sponsor id="cn2">Science and Technology Program of Beijing Municipality</contract-sponsor>
<counts>
<fig-count count="6"/>
<table-count count="4"/>
<equation-count count="0"/>
<ref-count count="42"/>
<page-count count="12"/>
<word-count count="6457"/>
</counts>
</article-meta>
</front>
<body>
<sec id="sec1" sec-type="intro">
<title>Introduction</title>
<p>The cell wall is particularly important in plant growth and development because it maintains the form of the plant cell, allows intercellular communication, responds to external environmental variables, and interacts with pathogenic microorganisms (<xref ref-type="bibr" rid="ref14">Keegstra, 2010</xref>; <xref ref-type="bibr" rid="ref28">Xin et al., 2010</xref>). The plant cell wall has a complicated and dynamic structure, which is mainly composed of polysaccharide polymer, protein and lignin. <italic>O</italic>-acetylation occurs extensively in the plant cell wall, most notably with hemicelluloses, pectins, and lignins. The replacements of <italic>O</italic>-acetyl group usually happen on various specific glycosyl residues of cell wall polysaccharides. In addition, cell wall polysaccharides can be either mono- or diacetylated, and the extent of <italic>O</italic>-acetylation depends on species, tissue type, and growth status of plants.</p>
<p>The biosynthetic pathway and function of <italic>O</italic>-acetylation of cell wall polysaccharides have not yet been fully understood. Modifications in <italic>O</italic>-acetylation levels are known to alter plant growth and development, as well as their defense against pathogens, and that this effect is most likely achieved by altering the cell wall structure. The REDUCED WALL ACETYLATION (RWA) protein, as well as the ALTERED XYLOGLUCAN9 protein and TRICHOME BIREFRINGENCE-LIKE (TBL) protein families, has been identified as being involved in the <italic>O</italic>-acetylation pathway of plant cell walls. RWA proteins could be acetyl donor transporters, transporting acetyl CoA into the Golgi apparatus (<xref ref-type="bibr" rid="ref18">Manabe et al., 2011</xref>, <xref ref-type="bibr" rid="ref19">2013</xref>). AXY9 protein may be required for <italic>O</italic>-acetylation of cell wall polysaccharides by producing acetylation intermediates (<xref ref-type="bibr" rid="ref20">Schultink et al., 2015</xref>).</p>
<p>Unlike the RWA and AXY9 proteins, a number of TBLs have been identified as polysaccharide acetyltransferases, catalyzing the <italic>O</italic>-acetylation of specific cell wall polymers including xylan (<xref ref-type="bibr" rid="ref23">Urbanowicz et al., 2015</xref>; <xref ref-type="bibr" rid="ref36">Zhong et al., 2017a</xref>; <xref ref-type="bibr" rid="ref34">Zhong et al., 2018a</xref>,<xref ref-type="bibr" rid="ref40">d</xref>), xyloglucan (<xref ref-type="bibr" rid="ref38">Zhong et al., 2018c</xref>,<xref ref-type="bibr" rid="ref39">e</xref>; <xref ref-type="bibr" rid="ref35">Zhong et al., 2020</xref>), mannan (<xref ref-type="bibr" rid="ref37">Zhong et al., 2018b</xref>), and pectin (<xref ref-type="bibr" rid="ref25">Vogel et al., 2004b</xref>; <xref ref-type="bibr" rid="ref3">Bischoff et al., 2010a</xref>; <xref ref-type="bibr" rid="ref21">Stranne et al., 2018a</xref>; <xref ref-type="bibr" rid="ref7">Chiniquy et al., 2019a</xref>). TBL proteins have conserved Asp-x-x-His (DxxH) motif and Gly-Asp-Ser (GDS) motif that is required for acetyltransferase activity (<xref ref-type="bibr" rid="ref4">Bischoff et al., 2010b</xref>), since a mutation in either the GDS or DXXH motif could cause TBL proteins to lose their function completely (<xref ref-type="bibr" rid="ref36">Zhong et al., 2017a</xref>; <xref ref-type="bibr" rid="ref39">Zhong et al., 2018e</xref>). Studies of <italic>tbl</italic> mutants in Arabidopsis have demonstrated that dwarfism, stem weakness, and stunted growth of plants are associated with the lack of the TBL genes (<xref ref-type="bibr" rid="ref3">Bischoff et al., 2010a</xref>; <xref ref-type="bibr" rid="ref29">Xiong et al., 2013</xref>; <xref ref-type="bibr" rid="ref20">Schultink et al., 2015</xref>), implying that TBL is critical for plant development. Besides, TBL proteins are related to abiotic stress in plants. Compared with wild-type Arabidopsis plant, the cold tolerance of <italic>esk1</italic> increased significantly (<xref ref-type="bibr" rid="ref28">Xin et al., 2010</xref>), while <italic>tbl10</italic> showed enhanced drought resistance (<xref ref-type="bibr" rid="ref21">Stranne et al., 2018a</xref>). Furthermore, TBL proteins have also been associated with plant defense against pathogens. The reduction of <italic>O</italic>-acetyl degree of <italic>pmr5</italic> in Arabidopsis may lead to its enhanced resistance to powdery mildew (<xref ref-type="bibr" rid="ref25">Vogel et al., 2004b</xref>; <xref ref-type="bibr" rid="ref7">Chiniquy et al., 2019a</xref>). According to a recent research, simultaneous mutation of the <italic>OsTBL1</italic> and <italic>OsTBL2</italic> genes in rice leads to lower acetylation levels and higher vulnerability to leaf blight disease (<xref ref-type="bibr" rid="ref10">Gao et al., 2017</xref>).</p>
<p>Rose (<italic>Rosa</italic> sp.) is the most important cut flower in the world, with 8,500 hectares of cut-flower rose cultivation worldwide, with an annual production of over 15 billion stems (<xref ref-type="bibr" rid="ref2">Bendahmane et al., 2013</xref>), and sales of more than $11 billion (<xref ref-type="bibr" rid="ref42">Zlesak, 2007</xref>). Gray mold caused by <italic>Botrytis cinerea</italic> is the most devastating disease mainly infecting the flower of rose and affects the production of cut rose all over the world (<xref ref-type="bibr" rid="ref13">Gleason and Helland, 2003</xref>). The cell wall is the initial barrier that pathogens meet when penetrating the plant, and alterations in cell wall structure might affect the plant&#x2019;s defense against these microbes. <italic>O</italic>-acetylation is one of the most important modifications of cell wall polymer. TBL proteins, as the main gene family involved in cell wall <italic>O</italic>-acetylation, may influence the resistance or susceptibility of plants to pathogen by varying the degree of cell wall acetylation. However, no research on the function of the TBL gene at the plant genome-wide level has been conducted thus far. We performed the first genome-wide analysis of the <italic>RcTBL</italic> family in rose in this study. Furthermore, a virus-induced gene silencing (VIGS) has confirmed that <italic>RcTBL16</italic> was involved in <italic>B. cinerea</italic> susceptibility.</p>
</sec>
<sec id="sec2" sec-type="materials|methods">
<title>Materials and Methods</title>
<sec id="sec3">
<title>Characterization of Putative TBL Proteins in Rose</title>
<p>We downloaded the complete rose genome sequence and CDS sequence from the website <ext-link xlink:href="https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/" ext-link-type="uri">https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/</ext-link> to construct a local genome database. In order to identify non-redundant <italic>RcTBL</italic> genes in rose genome, the HMM profile of the PC-Esterase domain was obtained from Pfam (PF13839<xref rid="fn0001" ref-type="fn"><sup>1</sup></xref>). Then, using this HMM profile as a query, by searching the rose genome, all sequences were confirmed to contain a PC-Esterase domain with an E value of &#x003C;1e<sup>-3</sup> in rose. The distribution of all <italic>RcTBL</italic> genes on chromosomes was mapped by mapchart 2.2 software.</p>
</sec>
<sec id="sec4">
<title>Gene Structure and Phylogenetic Analyses</title>
<p>The gene structure map of <italic>RcTBL</italic> was completed using TBtools (<xref ref-type="bibr" rid="ref6">Chen et al., 2018</xref>) by means of the rose genome annotation file and protein sequences. Multiple comparisons of <italic>RcTBL</italic> amino acids (aa) were performed using the ClustalW default parameters. A phylogenetic analysis of <italic>RcTBL</italic>s then was carried out in MEGA-6.0 software by the maximum likelihood (ML) method, with 1,000 bootstrap replications, JTT with Freqs (+F) model and 50% partial deletion. Other parameters were set by default. MEGA 6.0 was also applied to construct the unrooted ML trees of TBL proteins from Arabidopsis and rose, the parameter settings being consistent with the separate phylogenetic analysis of <italic>RcTBL</italic>s.</p>
</sec>
<sec id="sec5">
<title>Collinearity Analyses</title>
<p>For the purpose of identifying the collinearity of <italic>RcTBL</italic>s, the genome sequence of rose was downloaded on a local server, and then we used a Multiple Collinearity Scan toolkit (<xref ref-type="bibr" rid="ref26">Wang et al., 2012</xref>) to determine the microsyntenic relationships between <italic>RcTBL</italic> genes. Furthermore, collinearity scanning (e-value of &#x003C;1e<sup>&#x2212;10</sup>) was used to evaluate the microsynteny relationships.</p>
</sec>
<sec id="sec6">
<title>Calculation of Ratios of Nonsynonymous (Ka) to Synonymous (Ks) Nucleotide Substitutions</title>
<p>We used TBtools (<xref ref-type="bibr" rid="ref6">Chen et al., 2018</xref>) to calculate Ks and Ka nucleotide substitution rates. The Ka/Ks ratio of duplicated gene pairs was calculated to determine the selection pattern driving the evolution of <italic>RcTBL</italic>.</p>
</sec>
<sec id="sec7">
<title>Expression of <italic>RcTBL</italic>s in Response to <italic>B. cinerea</italic></title>
<p>RNA-Seq data from rose petals under <italic>B. cinerea</italic> infection were obtained from the National Center for Biotechnology Information database as accession number PRJNA414570 (<xref ref-type="bibr" rid="ref15">Liu et al., 2018</xref>). The materials for RNA-seq are rose petal discs infected with <italic>B. cinerea</italic> at 30h post inoculation (hpi) and 48hpi, with three biological repeats for both infected and control treatments at each time point. Clean sequencing reads were mapped to the <italic>Rosa chinensis</italic> &#x2018;Old Blush&#x2019; reference genome.<xref rid="fn0002" ref-type="fn"><sup>2</sup></xref> We calculated the gene expression levels of <italic>RcTBL</italic>s by Reads per kb per million reads and performed a Log2 fold change-based differentially expressed gene analysis by DEseq2.</p>
<p>For validating the RNA-Seq outcomes, RT-qPCR was used to analyze the expression of five <italic>RcTBL</italic> genes. Total RNA was extracted from rose petals at 30hpi and 48hpi, respectively. As described previously (<xref ref-type="bibr" rid="ref27">Wu et al., 2016</xref>), the hot borate method was used to extract total RNA. Then, first-strand cDNA was synthesized using HiScript II Q Select RT SuperMix (Vazyme) in a 20-&#x03BC;l reaction volume with 1&#x03BC;g of DNase-treated RNA. RT-qPCR reaction was run using SYBR Green Master Mix (Takara) and detection was achieved in a StepOnePlus real-time PCR system (Thermo Fisher Scientific). We used <italic>RcUBI2</italic> as an internal control and conducted expression analysis using the delta&#x2013;delta-Ct method of calculation. All primers used as RT-qPCR are listed in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S1</xref>.</p>
</sec>
<sec id="sec8">
<title>VIGS and <italic>B. cinerea</italic> Inoculation Assays</title>
<p>In order to obtain the <italic>pTRV2-RcTBL</italic> constructs, a~200bp fragment from the coding region of <italic>RcTBL</italic>s was amplified with specific primer pairs and subsequently cloned into the <italic>pTRV2</italic> vector (<xref ref-type="bibr" rid="ref16">Liu et al., 2002</xref>). VIGS was established as previously described (<xref ref-type="bibr" rid="ref5">Cao et al., 2019</xref>). Briefly, separated petals were obtained from the outermost whorls of cut roses in the second stage of flowering. A 15mm disc was then punched from the center of each petal. <italic>Agrobacterium tumefaciens</italic> consisting of <italic>pTRV1</italic> and <italic>pTRV2</italic> constructs were mixed in a 1:1 ratio and vacuumed infiltrated into petal discs. Petals were inoculated with <italic>B. cinerea</italic> on day 6 after TRV infection and photographed 60h later to obtain images with disease lesions, which were statistically analyzed by ImageJ. Each gene was silenced at least three times with 48 petals as a replicate. Student&#x2019;s <italic>t</italic> test was performed to determine the significance of lesion size. After photographing, the petal samples were collected for further validating of silencing efficiency by RT-qPCR. The primers used to detect silencing efficiency of <italic>RcTBL16</italic> or <italic>RcTBL35</italic> are the same primers as those used to detect expression in response to <italic>B. cinerea</italic>, and listed in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S1</xref>.</p>
</sec>
</sec>
<sec id="sec9" sec-type="results">
<title>Results</title>
<sec id="sec10">
<title>Identification of <italic>RcTBL</italic> Genes in Rose</title>
<p>As previously stated, the TBL protein family is distinguished by a conserved GDS signature and DXXH motif, as well as an N-terminal transmembrane domain in most of the cases (<xref ref-type="bibr" rid="ref3">Bischoff et al., 2010a</xref>,<xref ref-type="bibr" rid="ref4">b</xref>). A total of 61 candidate RcTBL proteins were obtained in rose by the Hidden Markov model (HMM) profile of PC-Esterase domain (PF13839) contained two conservative motifs of the TBL protein family. All candidate sequences less than 150 amino acids and without the complete conserved motifs were removed; finally, we obtained a total of 50 RcTBLs.</p>
<p>All <italic>RcTBL</italic>s can be mapped to rose chromosomes; we designated the genes <italic>RcTBL01</italic> to <italic>RcTBL50</italic> according to their chromosome order. The protein length of RcTBLs varies greatly. Of the 50 RcTBLs, RcTBL23 is the longest protein with 630 aa, while the shortest is RcTBL15 with 154 aa. The average length of proteins in RcTBL family is 409 aa. Details of the <italic>RcTBL</italic> genes, with gene number, chromosomal location, introns, exons, CDS and aa length are listed in <xref rid="tab1" ref-type="table">Table 1</xref>.</p>
<table-wrap position="float" id="tab1">
<label>Table 1</label>
<caption><p>Members of the <italic>RcTBL</italic> gene family as predicted in <italic>Rosa chinensis</italic> genome sequence.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" valign="top">Gene</th>
<th align="left" valign="top">Accession number<xref rid="tfn1" ref-type="table-fn"><sup>1</sup></xref>
</th>
<th align="center" valign="top">Chr<xref rid="tfn2" ref-type="table-fn"><sup>2</sup></xref></th>
<th align="left" valign="top">Position<xref rid="tfn3" ref-type="table-fn"><sup>3</sup></xref></th>
<th align="center" valign="top">Intron</th>
<th align="center" valign="top">Exon</th>
<th align="center" valign="top">CDS(bp)</th>
<th align="center" valign="top">Amino acids</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="middle">RcTBL01</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0332411</td>
<td align="center" valign="top">1</td>
<td align="center" valign="middle">23.56</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,152</td>
<td align="center" valign="middle">383</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL02</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0359011</td>
<td align="center" valign="top">1</td>
<td align="center" valign="middle">50.99</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">1,368</td>
<td align="center" valign="middle">455</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL03</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0370451</td>
<td align="center" valign="top">1</td>
<td align="center" valign="middle">59.94</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,482</td>
<td align="center" valign="middle">493</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL04</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0371061</td>
<td align="center" valign="top">1</td>
<td align="center" valign="middle">60.41</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">6</td>
<td align="center" valign="top">1,302</td>
<td align="center" valign="middle">433</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL05</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0375151</td>
<td align="center" valign="top">1</td>
<td align="center" valign="middle">62.68</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">1788</td>
<td align="center" valign="middle">595</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL06</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0095401</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">8.34</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,599</td>
<td align="center" valign="middle">532</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL07</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0120351</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">33.07</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">1,365</td>
<td align="center" valign="middle">454</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL08</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0121951</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">34.79</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">1,509</td>
<td align="center" valign="middle">502</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL09</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0129071</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">44.73</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,122</td>
<td align="center" valign="middle">373</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL10</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0131401</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">47.54</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,056</td>
<td align="center" valign="middle">351</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL11</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0131411</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">47.57</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">768</td>
<td align="center" valign="middle">255</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL12</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0131441</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">47.65</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,092</td>
<td align="center" valign="middle">363</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL13</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0131461</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">47.69</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">624</td>
<td align="center" valign="middle">207</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL14</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0150421</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">68.08</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,146</td>
<td align="center" valign="middle">381</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL15</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0163731</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">79.08</td>
<td align="center" valign="top">0</td>
<td align="center" valign="top">1</td>
<td align="center" valign="top">465</td>
<td align="center" valign="middle">154</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL16</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0163771</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">79.09</td>
<td align="center" valign="top">1</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">1,275</td>
<td align="center" valign="middle">424</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL17</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0163781</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">79.10</td>
<td align="center" valign="top">1</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">1,350</td>
<td align="center" valign="middle">449</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL18</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0170621</td>
<td align="center" valign="top">2</td>
<td align="center" valign="middle">84.51</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">1,278</td>
<td align="center" valign="middle">425</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL19</td>
<td align="left" valign="middle">RchiOBHm_Chr3g0461751</td>
<td align="center" valign="top">3</td>
<td align="center" valign="middle">9.73</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">6</td>
<td align="center" valign="top">1,332</td>
<td align="center" valign="middle">443</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL20</td>
<td align="left" valign="middle">RchiOBHm_Chr3g0461761</td>
<td align="center" valign="top">3</td>
<td align="center" valign="middle">9.74</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,425</td>
<td align="center" valign="middle">474</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL21</td>
<td align="left" valign="middle">RchiOBHm_Chr3g0462741</td>
<td align="center" valign="top">3</td>
<td align="center" valign="middle">10.34</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">6</td>
<td align="center" valign="top">1,308</td>
<td align="center" valign="middle">435</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL22</td>
<td align="left" valign="middle">RchiOBHm_Chr3g0474891</td>
<td align="center" valign="top">3</td>
<td align="center" valign="middle">20.68</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">792</td>
<td align="center" valign="middle">263</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL23</td>
<td align="left" valign="middle">RchiOBHm_Chr3g0479331</td>
<td align="center" valign="top">3</td>
<td align="center" valign="middle">25.17</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1893</td>
<td align="center" valign="middle">630</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL24</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0398501</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">15.04</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,311</td>
<td align="center" valign="middle">436</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL25</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0398521</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">15.07</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,533</td>
<td align="center" valign="middle">510</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL26</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0417821</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">43.12</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">1,365</td>
<td align="center" valign="middle">454</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL27</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0424421</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">50.04</td>
<td align="center" valign="top">0</td>
<td align="center" valign="top">1</td>
<td align="center" valign="top">1,056</td>
<td align="center" valign="middle">351</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL28</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0433581</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">57.66</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">555</td>
<td align="center" valign="middle">184</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL29</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0442021</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">63.74</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1863</td>
<td align="center" valign="middle">620</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL30</td>
<td align="left" valign="middle">RchiOBHm_Chr4g0444361</td>
<td align="center" valign="top">4</td>
<td align="center" valign="middle">65.13</td>
<td align="center" valign="top">1</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">1,353</td>
<td align="center" valign="middle">450</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL31</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0010331</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">6.84</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,113</td>
<td align="center" valign="middle">370</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL32</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0025161</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">19.14</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">549</td>
<td align="center" valign="middle">182</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL33</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0029581</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">23.19</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,137</td>
<td align="center" valign="middle">378</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL34</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0029591</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">23.20</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,023</td>
<td align="center" valign="middle">340</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL35</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0029601</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">23.20</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,143</td>
<td align="center" valign="middle">380</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL36</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0029611</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">23.21</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,086</td>
<td align="center" valign="middle">361</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL37</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0031471</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">25.06</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,251</td>
<td align="center" valign="middle">416</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL38</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0070191</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">76.02</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,161</td>
<td align="center" valign="middle">386</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL39</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0081011</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">87.06</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">549</td>
<td align="center" valign="middle">182</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL40</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0081071</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">87.07</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">6</td>
<td align="center" valign="top">1,638</td>
<td align="center" valign="middle">545</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL41</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0081121</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">87.16</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,578</td>
<td align="center" valign="middle">525</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL42</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0081131</td>
<td align="center" valign="top">5</td>
<td align="center" valign="middle">87.16</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1761</td>
<td align="center" valign="middle">586</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL43</td>
<td align="left" valign="middle">RchiOBHm_Chr6g0247241</td>
<td align="center" valign="top">6</td>
<td align="center" valign="middle">3.06</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">6</td>
<td align="center" valign="top">1,260</td>
<td align="center" valign="middle">419</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL44</td>
<td align="left" valign="middle">RchiOBHm_Chr6g0247271</td>
<td align="center" valign="top">6</td>
<td align="center" valign="middle">3.12</td>
<td align="center" valign="top">6</td>
<td align="center" valign="top">7</td>
<td align="center" valign="top">1,317</td>
<td align="center" valign="middle">438</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL45</td>
<td align="left" valign="middle">RchiOBHm_Chr6g0269281</td>
<td align="center" valign="top">6</td>
<td align="center" valign="middle">26.54</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">1,194</td>
<td align="center" valign="middle">397</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL46</td>
<td align="left" valign="middle">RchiOBHm_Chr6g0277131</td>
<td align="center" valign="top">6</td>
<td align="center" valign="middle">39.52</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">1,323</td>
<td align="center" valign="middle">440</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL47</td>
<td align="left" valign="middle">RchiOBHm_Chr6g0291221</td>
<td align="center" valign="top">6</td>
<td align="center" valign="middle">54.42</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">1,302</td>
<td align="center" valign="middle">433</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL48</td>
<td align="left" valign="middle">RchiOBHm_Chr7g0195391</td>
<td align="center" valign="top">7</td>
<td align="center" valign="middle">13.24</td>
<td align="center" valign="top">2</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">1,332</td>
<td align="center" valign="middle">443</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL49</td>
<td align="left" valign="middle">RchiOBHm_Chr7g0217351</td>
<td align="center" valign="top">7</td>
<td align="center" valign="middle">35.23</td>
<td align="center" valign="top">3</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">756</td>
<td align="center" valign="middle">251</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL50</td>
<td align="left" valign="middle">RchiOBHm_Chr7g0241111</td>
<td align="center" valign="top">7</td>
<td align="center" valign="middle">67.11</td>
<td align="center" valign="top">4</td>
<td align="center" valign="top">5</td>
<td align="center" valign="top">1,542</td>
<td align="center" valign="middle">513</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn id="tfn1"><label>1</label><p><italic>Available at:</italic> <ext-link xlink:href="https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/" ext-link-type="uri"><italic>https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/</italic></ext-link></p></fn>
<fn id="tfn2"><label>2</label><p><italic>Chromosome</italic>.</p></fn>
<fn id="tfn3"><label>3</label><p><italic>Starting position (Mb)</italic>.</p></fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="sec11">
<title>Chromosomal Locations, Whole-Genome Duplication, and Microsynteny</title>
<p>All 50 <italic>RcTBL</italic> genes were distributed unevenly across seven rose chromosomes (<xref rid="fig1" ref-type="fig">Figure 1</xref>), with chromosome 2 having the highest density, gathering 13 <italic>RcTBL</italic> genes, followed by chromosome 5 with 12 <italic>RcTBL</italic> genes clustered on it, and chromosome 7 having the fewest <italic>RcTBL</italic> genes with only three members. We further investigated the duplication events in <italic>RcTBL</italic>s. Tandemly duplicated genes were defined as arrays of two or more homologous genes in the 100kb range. Three <italic>RcTBL</italic> gene pairs were discovered in the rose genome, each on a different chromosome, suggesting that segmental duplication occurs within these regions in rose. Collinearity analyses of the <italic>RcTBL</italic> genes on the chromosome are depicted in <xref rid="fig2" ref-type="fig">Figure 2</xref>.</p>
<fig position="float" id="fig1">
<label>Figure 1</label>
<caption><p>Chromosome localization of rose TBL family members. The distribution of <italic>RcTBL</italic>s is shown on the seven chromosomes of <italic>Rose chinensis</italic>. The starting position (bp) of each <italic>RcTBL</italic> is listed on the left side of the chromosomes.</p></caption>
<graphic xlink:href="fpls-12-738880-g001.tif"/>
</fig>
<fig position="float" id="fig2">
<label>Figure 2</label>
<caption><p>Microsyntenic analyses of the rose TBL protein family members in the <italic>R. chinensis</italic> genome. Circular visualization of rose TBL protein family members is mapped onto different chromosomes by using Circos. The red lines indicate rose <italic>TBL</italic> genes with a syntenic relationship. The gray lines represent all syntenic blocks in the genome of <italic>R. chinensis</italic>.</p></caption>
<graphic xlink:href="fpls-12-738880-g002.tif"/>
</fig>
<p>To explore the selective constraints among duplicated <italic>RcTBL</italic> genes, the ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions (Ka/Ks ratio) of three pairs of duplicated genes (<xref rid="tab2" ref-type="table">Table 2</xref>) was calculated. Typically, Ka/Ks &#x003E;1 is consistent with positive selection, while Ka/Ks &#x003C;1 indicates purifying selection. Ka/Ks &#x003C;1 for all three duplicated gene pairs (<xref rid="tab2" ref-type="table">Table 2</xref>) suggested that the primary driver of gene evolution in the <italic>RcTBL</italic> family was purifying selection.</p>
<table-wrap position="float" id="tab3">
<label>Table 2</label>
<caption><p>Duplication analysis of the <italic>RcTBL</italic> gene family.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" valign="top">Gene 1</th>
<th align="center" valign="top">Gene 2</th>
<th align="center" valign="top">Ka</th>
<th align="center" valign="top">Ks</th>
<th align="center" valign="top">Ka_Ks</th>
<th align="center" valign="top">Effective Len</th>
<th align="center" valign="top">Average S-sites</th>
<th align="center" valign="top">Average N-sites</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="top">RcTBL18</td>
<td align="center" valign="top">RcTBL30</td>
<td align="center" valign="middle">0.645328</td>
<td align="center" valign="middle">NaN</td>
<td align="center" valign="middle">NaN</td>
<td align="center" valign="middle">1,257</td>
<td align="center" valign="middle">275.3333333</td>
<td align="center" valign="middle">981.6666667</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL09</td>
<td align="center" valign="top">RcTBL31</td>
<td align="center" valign="middle">0.327007</td>
<td align="center" valign="middle">2.080681</td>
<td align="center" valign="middle">0.157164</td>
<td align="center" valign="middle">1,107</td>
<td align="center" valign="middle">252.4166667</td>
<td align="center" valign="middle">854.5833333</td>
</tr>
<tr>
<td align="left" valign="top">RcTBL02</td>
<td align="center" valign="top">RcTBL48</td>
<td align="center" valign="middle">0.317547</td>
<td align="center" valign="middle">1.749673</td>
<td align="center" valign="middle">0.181489</td>
<td align="center" valign="middle">1,299</td>
<td align="center" valign="middle">283.75</td>
<td align="center" valign="middle">1015.25</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="sec12">
<title>Phylogenetic and Gene Structural Analysis of Rose TBL Genes</title>
<p>A total of 46 TBLs were identified on <italic>Arabidopsis thaliana</italic> and many of them have been established as <italic>O</italic>-acetyltransferases or potential <italic>O</italic>-acetyltransferase genes (<xref rid="tab3" ref-type="table">Table 3</xref>). To evaluate the relationship between the TBL proteins of rose and <italic>A. thaliana</italic>, a compound phylogenetic tree was constructed using the full-length protein sequences of 46 Arabidopsis and 50 rose TBLs by the ML method. We found that most of the Arabidopsis TBL proteins had at least one rose homologue. <italic>AtTBL</italic> members identified as affecting the <italic>O</italic>-acetylation of xyloglucan, xylan, mannan, and pectin, respectively, were clustered in different branches, suggesting the correctness of our evolutionary tree (<xref rid="fig3" ref-type="fig">Figure 3</xref>).</p>
<fig position="float" id="fig3">
<label>Figure 3</label>
<caption><p>Phylogenetic analyses of TBL protein family in rose with <italic>Arabidopsis thaliana</italic> TBL protein family. Genes marked with pink have been shown to be involved in <italic>O</italic>-acetylation of cell wall polysaccharides in <italic>A. thaliana</italic> (<xref rid="tab2" ref-type="table">Table 3</xref>); genes marked with green may be involved in the defense of roses against <italic>B. cinerea</italic> and were knocked down by virus-induced gene silencing (VIGS) in rose petals. Arrows refer to the well-known TBL proteins in Arabidopsis. The bootstrap values are indicated on the nodes of the branches.</p></caption>
<graphic xlink:href="fpls-12-738880-g003.tif"/>
</fig>
<table-wrap position="float" id="tab2">
<label>Table 3</label>
<caption><p>Arabidopsis TBL family genes involved in acetylation.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" valign="top">Gene name</th>
<th align="left" valign="top">Gene ID</th>
<th align="left" valign="top">Polysaccharides</th>
<th align="left" valign="top">References</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="top">AtTBL3</td>
<td align="left" valign="top">At5G01360</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref33">Yuan et al., 2016c</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL28</td>
<td align="left" valign="top">At2G40150</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref36">Zhong et al., 2017a</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL29/ESK1</td>
<td align="left" valign="top">At3G55990</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref29">Xiong et al., 2013</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL30</td>
<td align="left" valign="top">At2G40160</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref36">Zhong et al., 2017a</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL31</td>
<td align="left" valign="top">At1G73140</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref33">Yuan et al., 2016c</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL32</td>
<td align="left" valign="top">At3G11030</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref31">Yuan et al., 2016a</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL33</td>
<td align="left" valign="top">At2G40320</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref31">Yuan et al., 2016a</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL34</td>
<td align="left" valign="top">At2G38320</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref32">Yuan et al., 2016b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL35</td>
<td align="left" valign="top">At5G01620</td>
<td align="left" valign="top">Xylan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref32">Yuan et al., 2016b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL19</td>
<td align="left" valign="top">AT5G15900</td>
<td align="left" valign="top">Xyloglucan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref35">Zhong et al., 2020</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL20</td>
<td align="left" valign="top">AT3G02440</td>
<td align="left" valign="top">Xyloglucan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref35">Zhong et al., 2020</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL21</td>
<td align="left" valign="top">AT5G15890</td>
<td align="left" valign="top">Xyloglucan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref35">Zhong et al., 2020</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL22/AXY4L</td>
<td align="left" valign="top">At3G28150</td>
<td align="left" valign="top">Xyloglucan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref11">Gille et al., 2011a</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL27/AXY4</td>
<td align="left" valign="top">At1G70230</td>
<td align="left" valign="top">Xyloglucan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref11">Gille et al., 2011a</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL23</td>
<td align="left" valign="top">At4G11090</td>
<td align="left" valign="top">Mannan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref37">Zhong et al., 2018b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL24</td>
<td align="left" valign="top">At4G23790</td>
<td align="left" valign="top">Mannan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref37">Zhong et al., 2018b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL25</td>
<td align="left" valign="top">At1G01430</td>
<td align="left" valign="top">Mannan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref37">Zhong et al., 2018b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL26</td>
<td align="left" valign="top">At4G01080</td>
<td align="left" valign="top">Mannan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref37">Zhong et al., 2018b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL10</td>
<td align="left" valign="top">At3G06080</td>
<td align="left" valign="top">Rhamnogalacturonan-I</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref22">Stranne et al., 2018b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">AtTBL44/PMR5</td>
<td align="left" valign="top">At5G58600</td>
<td align="left" valign="top">Homogalacturonan</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref8">Chiniquy et al., 2019b</xref>
</td>
</tr>
<tr>
<td align="left" valign="top">TBR/TBL46</td>
<td align="left" valign="top">TBR/TBL46</td>
<td align="left" valign="top">Pectin</td>
<td align="left" valign="top">
<xref ref-type="bibr" rid="ref3">Bischoff et al., 2010a</xref>
</td>
</tr>
</tbody>
</table>
</table-wrap>
<p>Analysis of the exon&#x2013;intron structure revealed that the intron structure of <italic>RcTBL</italic>s were highly variable, ranging from 1 to 6, with the largest number (23) of <italic>RcTBL</italic>s containing four introns. In addition, the length of <italic>RcTBL</italic> introns was extremely varied, ranging from tens to thousands of nucleotides. <italic>RcTBL35</italic> contained the longest intron (4,191bp), while the shortest intron (69bp) was present on <italic>RcTBL36</italic> (<xref rid="fig4" ref-type="fig">Figure 4</xref>).</p>
<fig position="float" id="fig4">
<label>Figure 4</label>
<caption><p>Phylogenetic analyses and gene structures of rose TBL proteins. Complete alignments of all rose TBL proteins were used to construct a phylogenetic tree using the maximum likelihood method. The bootstrap values are indicated on the nodes of the branches. Exon&#x2013;intron structure of <italic>RcTBLs</italic> is shown in the middle part of the figure, and the green boxes, yellow boxes, and gray lines represent UTRs, exons, and introns, respectively. Transmembrane and conserved domain of <italic>RcTBLs</italic> are displayed in the right part of the figure, and the green boxes, yellow boxes, and pink boxes represent PC-Esterase domain, transmembrane domain, and PMR5N domain, respectively. The scale on the bottom is provided as a reference.</p></caption>
<graphic xlink:href="fpls-12-738880-g004.tif"/>
</fig>
<p>The protein sequences of RcTBLs were examined with Pfam and all 50 candidate genes had the PC-esterase domain. Surprisingly, 88% of RcTBLs possessed a cys-rich domain called the PMR5N domain in Pfam (PF14416) that preceded the PC-esterase domain, implying that it could be a crucial structural element of the TBL family. Furthermore, 64% of all 50 RcTBL candidates had at least one transmembrane domain, with RcTBL40 having two transmembrane domains, and 18 RCTBLs had no transmembrane domain (<xref rid="fig4" ref-type="fig">Figure 4</xref>).</p>
</sec>
<sec id="sec13">
<title>The Expression of <italic>RcTBL</italic> Genes in Response to <italic>B. cinerea</italic> Infection</title>
<list list-type="simple">
<list-item>
<p>Growing evidence has shown that TBL plays an important role in pathogen defense. In order to investigate the role of <italic>RcTBL</italic>s in <italic>B. cinerea</italic> resistance, we obtained RNAseq transcriptomics data from rose petals at 30hpi (hours post-inoculation) and 48hpi (<xref ref-type="bibr" rid="ref15">Liu et al., 2018</xref>). The 30hpi represents the early response to the infection of <italic>B. cinerea</italic>, while the 48hpi corresponds to the late response. A total of 13 <italic>RcTBL</italic> genes showed significant changes in expression and, interestingly, they were mainly down-regulated in expression (<xref rid="tab4" ref-type="table">Table 4</xref>). Among them, <italic>RcTBL12</italic> and <italic>RcTBL35</italic> were both considerably down-regulated at 30hpi and 48hpi, whereas <italic>RcTBL02</italic>, <italic>RcTBL04</italic>, <italic>RcTBL05</italic>, <italic>RcTBL16</italic>, and <italic>RcTBL36</italic> were only significantly down-regulated at 30hpi, <italic>RcTBL23</italic>, <italic>RcTBL38</italic>, and <italic>RcTBL48</italic> were only significantly down-regulated at 48hpi. Surprisingly, <italic>RcTBL18</italic> expression was dramatically decreased at 30hpi but significantly increased at 48hpi, whereas <italic>RcTBL06</italic> and <italic>RcTBL09</italic> expression was greatly increased at 48hpi. These genes, which are strongly activated by gray mold, could be crucial in rose resistance to <italic>B. cinerea</italic> infection. To further validate the RNA-seq expression profile, the expressions of five <italic>RcTBL</italic>s were examined using RT-qPCR. The RT-qPCR analysis results were found associated with the transcriptome analysis expression patterns (<xref rid="fig5" ref-type="fig">Figure 5</xref>).</p>
</list-item>
</list>
<table-wrap position="float" id="tab4">
<label>Table 4</label>
<caption><p>Expression patterns of <italic>RcTBL</italic> genes under infection of <italic>B. cinerea</italic><xref rid="tfn4" ref-type="table-fn"><sup>1</sup></xref>.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" valign="top">Gene<xref rid="tfn5" ref-type="table-fn"><sup>2</sup></xref>
</th>
<th align="left" valign="top">Accession number</th>
<th align="center" valign="top">Log<xref rid="tfn5" ref-type="table-fn"><sup>2</sup></xref>ratio 30hpi</th>
<th align="center" valign="top">Log<xref rid="tfn5" ref-type="table-fn"><sup>2</sup></xref>ratio 48hpi<xref rid="tfn6" ref-type="table-fn"><sup>3</sup></xref></th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="middle"><bold>RcTBL02</bold></td>
<td align="left" valign="middle">RchiOBHm_Chr1g0359011</td>
<td align="center" valign="middle">&#x2212;1.450</td>
<td align="center" valign="middle">&#x2013;</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL04</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0371061</td>
<td align="center" valign="middle">&#x2212;1.14643</td>
<td align="center" valign="middle">0.405416</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL05</td>
<td align="left" valign="middle">RchiOBHm_Chr1g0375151</td>
<td align="center" valign="middle">&#x2212;1.210</td>
<td align="center" valign="middle">&#x2212;0.707</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL06</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0095401</td>
<td align="center" valign="middle">&#x2212;0.366</td>
<td align="center" valign="middle">1.237</td>
</tr>
<tr>
<td align="left" valign="middle"><bold>RcTBL09</bold></td>
<td align="left" valign="middle">RchiOBHm_Chr2g0129071</td>
<td align="center" valign="middle">0.726</td>
<td align="center" valign="middle">1.139</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL12</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0131441</td>
<td align="center" valign="middle">&#x2212;1.646</td>
<td align="center" valign="middle">&#x2212;1.875</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL16</td>
<td align="left" valign="middle">RchiOBHm_Chr2g0163771</td>
<td align="center" valign="middle">&#x2212;2.239</td>
<td align="center" valign="middle">&#x2013;</td>
</tr>
<tr>
<td align="left" valign="middle"><bold>RcTBL18</bold></td>
<td align="left" valign="middle">RchiOBHm_Chr2g0170621</td>
<td align="center" valign="middle">&#x2212;1.639</td>
<td align="center" valign="middle">1.416</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL23</td>
<td align="left" valign="middle">RchiOBHm_Chr3g0479331</td>
<td align="center" valign="middle">&#x2212;0.682</td>
<td align="center" valign="middle">&#x2212;1.012</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL35</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0029601</td>
<td align="center" valign="middle">&#x2212;2.017</td>
<td align="center" valign="middle">&#x2212;1.643</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL36</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0029611</td>
<td align="center" valign="middle">&#x2212;1.079</td>
<td align="center" valign="middle">&#x2013;</td>
</tr>
<tr>
<td align="left" valign="middle">RcTBL38</td>
<td align="left" valign="middle">RchiOBHm_Chr5g0070191</td>
<td align="center" valign="middle">&#x2212;0.505</td>
<td align="center" valign="middle">&#x2212;2.356</td>
</tr>
<tr>
<td align="left" valign="middle"><bold>RcTBL48</bold></td>
<td align="left" valign="middle">RchiOBHm_Chr7g0195391</td>
<td align="center" valign="middle">&#x2212;0.361</td>
<td align="center" valign="middle">&#x2212;1.129</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn id="tfn4"><label>1</label><p><italic>The log2 transformed expression profiles were obtained from the RNA-seq dataset (<xref ref-type="bibr" rid="ref15">Liu et al., 2018</xref>)</italic>.</p></fn>
<fn id="tfn5"><label>2</label><p><italic>The RcTBLs undergo duplicate events are marked in bold</italic>.</p></fn>
<fn id="tfn6"><label>3</label><p><italic>A dash &#x2018;-&#x2019; means that data are not available</italic>.</p></fn>
</table-wrap-foot>
</table-wrap>
<fig position="float" id="fig5">
<label>Figure 5</label>
<caption><p>Validation of RNA-Seq results using RT-qPCR. <italic>RcUBI2</italic> was used as an internal control. Expression profile data of five <italic>RcTBL</italic> genes at 30hpi and 48hpi after <italic>B. cinerea</italic> inoculation were obtained using RT-qPCR. Values are the means of three technical replicates &#x00B1; SD. The used primers are listed in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S1</xref>.</p></caption>
<graphic xlink:href="fpls-12-738880-g005.tif"/>
</fig>
</sec>
<sec id="sec14">
<title><italic>RcTBL16</italic> Involving in the Defense of Rose Against <italic>B. cinerea</italic></title>
<list list-type="simple">
<list-item>
<p>The elucidation of gene expression patterns can provide important clues about gene function. Based on the expression results in response to <italic>B. cinerea</italic>, 13 <italic>RcTBL</italic>s with significant differential expression were considered as potential candidates participating in rose against <italic>B. cinerea</italic>. Their potential role in resistance to this fungus was further illustrated by the reduced expression in rose petals by VIGS. We selected <italic>RcTBL16</italic> and <italic>RcTBL35</italic> as candidate genes to explore the relationship between TBL family and rose resistance to <italic>B. cinerea</italic>, because (1) apart from <italic>RcTBL38</italic> (a <italic>PMR5</italic> homolog), <italic>RcTBL16</italic> and <italic>RcTBL35</italic> were the two of maximum down-regulated expressed <italic>RcTBL</italic> genes in response to <italic>B. cinerea</italic> (<xref rid="tab4" ref-type="table">Table 4</xref>), and the results of RT-qPCR support this result (<xref rid="fig5" ref-type="fig">Figure 5</xref>); (2) both <italic>RcTBL16</italic> and <italic>RcTBL35</italic> are down-regulated in expression at 30hpi, which represent an early stages of <italic>B. cinerea</italic> infection (<xref ref-type="bibr" rid="ref15">Liu et al., 2018</xref>).</p>
</list-item>
<list-item>
<p>In order to silence <italic>RcTBL16</italic> and <italic>RcTBL35</italic>, we cloned approximately 200bp fragments of them into the <italic>pTRV2</italic> vector to generate <italic>pTRV2-RcTBL16</italic> and <italic>pTRV2-RcTBL35</italic>. Next, <italic>Agrobacterium tumefaciens</italic> carrying <italic>pTRV2-RcTBL16</italic>, <italic>pTRV2-RcTBL35</italic> and <italic>pTRV1</italic> were co-infiltrated into the rose petals to generate silent rose petals. Then, the infiltrated rose petal discs were put on agar medium and inoculated with <italic>B. cinerea</italic>. Comparing the control inoculated with <italic>TRV-GFP</italic>, petals inoculated with <italic>TRV-RcTBL16</italic> showed notably reduced disease symptoms, whereas the area of disease spots on petals inoculated with <italic>TRV-RcTBL35</italic> had no significantly changes (<xref rid="fig6" ref-type="fig">Figure 6</xref>). This result indicated that <italic>RcTBL16</italic> is a susceptibility gene involved in <italic>Botrytis</italic>-rose interaction.</p>
</list-item>
</list>
<fig position="float" id="fig6">
<label>Figure 6</label>
<caption><p>Functional analysis of <italic>RcTBL16</italic>. <bold>(A)</bold> Altered <italic>B. cinerea</italic> resistance upon silencing of <italic>RcTBL16</italic> and unaltered <italic>B. cinerea</italic> resistance upon silenced <italic>RcTBL35</italic> at 60hpi post-inoculation. <bold>(B)</bold> Quantification of <italic>B. cinerea</italic> disease lesions on <italic>TRV-RcTBL16</italic>, <italic>TRV-RcTBL35</italic>, and <italic>TRV-GFP</italic>-inoculated rose petal discs. The graph shows the lesion size from one replicate out of four (<italic>n</italic>&#x2265;48) with the standard deviation. <bold>(C)</bold> Quantification of <italic>RcTBL16</italic> expression in <italic>TRV-RcTBL16</italic> and <italic>TRV-GFP</italic>-inoculated petal discs. <bold>(D)</bold> Quantification of <italic>RcTBL35</italic> expression in <italic>TRV-RcTBL35</italic> and <italic>TRV- GFP</italic>-inoculated petal discs. Statistical analyses were performed using Student&#x2019;s <italic>t</italic> test; <sup>&#x002A;</sup><italic>p</italic>&#x003C;0.01, <sup>&#x002A;</sup><italic>p</italic>&#x003C;0.05.</p></caption>
<graphic xlink:href="fpls-12-738880-g006.tif"/>
</fig>
</sec>
</sec>
<sec id="sec15" sec-type="discussions">
<title>Discussion</title>
<p><italic>O</italic>-acetylation is a common modification on plant cell walls and is essential for the stability of the polysaccharide network, with a small amount of acetylation modification affecting plant growth and susceptibility to pathogens. TBL is the largest protein family involved in <italic>O</italic>-acetylation in plants. There are 46 TBLs in Arabidopsis (<xref ref-type="bibr" rid="ref3">Bischoff et al., 2010a</xref>), 18 of which have been identified as <italic>O</italic>-acetyltransferases, involved in the <italic>O</italic>-acetylation of xylan xyloglucan mannan and pectin respectively (<xref rid="tab3" ref-type="table">Table 3</xref>). Several TBL proteins from rice and poplar have also been shown to be xylan <italic>O</italic>-acetyltransferases (<xref ref-type="bibr" rid="ref34">Zhong et al., 2018a</xref>,<xref ref-type="bibr" rid="ref40">d</xref>). However, there is still a gap in the comprehensive analysis of the rose TBL gene family, and their function remains to be discovered. Rose genome sequencing project was completed in 2018, enabling genome-wide analysis of the <italic>RcTBL</italic> gene family. In this study, we have comprehensively analyzed the <italic>RcTBL</italic> family, including phylogeny, gene structure, chromosomal location, gene duplication events, sequence characterization, and analysis of expression profiles.</p>
<p>We identified 50 rose TBLs, more than Arabidopsis (46) (<xref ref-type="bibr" rid="ref3">Bischoff et al., 2010a</xref>) but less than poplar (64) (<xref ref-type="bibr" rid="ref40">Zhong et al., 2018d</xref>), rice (66) (<xref ref-type="bibr" rid="ref10">Gao et al., 2017</xref>), tomatoes (69) (<xref ref-type="bibr" rid="ref35">Zhong et al., 2020</xref>), which indicates that TBL protein family has expanded to varying degrees in different plants during the evolution. In our structural analysis, we found that in addition to the PC-esterase domain, RcTBLs have a cys-rich domain, namely PMR5N domain, which may be another vital characteristic of the TBL family. Gene duplication plays a very important role in the expansion of gene families. Checking the phylogenetic relationships of TBL between rose and Arabidopsis showed that most evolved branches contained different amounts of AtTBL and RcTBL proteins, suggesting that the two species displayed conserved evolution.</p>
<p>The composition of the cell wall is closely correlated with fungal disease resistance, and altered levels of cell wall polysaccharide <italic>O</italic>-acetylation modification can lead to altered plant resistance to fungi. In some cases, a reduction in the level of acetylation enhances plant resistance to pathogens. For instance, Arabidopsis <italic>rwa2</italic> showed a 20% reduction in the degree of cell wall polysaccharide acetylation modification and was more resistant to <italic>B. cinerea</italic> than wild type. In this study, we also found <italic>RcTBL16</italic> negatively regulating resistance to gray mold in rose. <italic>PMR5</italic>, a member of the TBL family, has the same performance in resisting powdery mildew in Arabidopsis (<xref ref-type="bibr" rid="ref24">Vogel et al., 2004a</xref>), by the <italic>O</italic>-acetylation modification of homogalacturonan (<xref ref-type="bibr" rid="ref7">Chiniquy et al., 2019a</xref>). Therefore, we consider that partial rose TBL genes may be involved in the susceptibility of rose to <italic>B. cinerea</italic> through acetylating cell wall.</p>
<p>It is clear that changes in the level of <italic>O</italic>-acetylation modification of cell walls can affect plant resistance or susceptibility to pathogens, but the exact mechanism remains a mystery at present. One hypothesis suggests that alterations in the polysaccharide composition of the cell wall will modify the cell wall integrity (CWI) system, thereby triggering plant defenses and activating specific defense responses (<xref ref-type="bibr" rid="ref1">Bacete et al., 2017</xref>). Alteration of cell wall xylan acetylation caused by <italic>ESK1</italic> impairment was accompanied by an enhanced accumulation of abscisic acid, the constitutive expression of genes encoding antibiotic peptides and enzymes involved in the biosynthesis of tryptophan-derived metabolites, and the accumulation of disease resistance-related secondary metabolites and different osmolites, implying that the damage to CWI triggers defense response of plant (<xref ref-type="bibr" rid="ref17">Lugan et al., 2010</xref>; <xref ref-type="bibr" rid="ref28">Xin et al., 2010</xref>; <xref ref-type="bibr" rid="ref30">Xu et al., 2014</xref>; <xref ref-type="bibr" rid="ref9">Escudero et al., 2017</xref>). However, it needs to be substantiated by stronger evidence. Overall, more research remains to be done on the certain mechanisms of TBL participant plant&#x2013;pathogen interactions, but there is no doubt that TBLs in rose is most possibly as a susceptibility factor for the resistance to gray mold, and this result will also provide clues for rose breeding application (i.e., enhancing persistent plant resistance by silencing or knocking out susceptibility genes).</p>
</sec>
<sec id="sec16" sec-type="conclusions">
<title>Conclusion</title>
<p>The study performed a genome-wide analysis of <italic>RcTBL</italic>s, including phylogenetic relationships, collinearity, and expression analysis. A total of 50 non-redundant <italic>RcTBL</italic> members were identified. The expression analysis showed that transcription regulation of several <italic>RcTBL</italic> was reduced by <italic>B. cinerea</italic> infection in rose petals. Based on these analyses and VIGS, we further demonstrated that <italic>RcTBL16</italic> was engaged in susceptibility of rose to gray mold. The information provided by these results can promote the further functional analysis of <italic>RcTBL</italic> genes and application in rose disease resistance breeding.</p>
</sec>
<sec id="sec17" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>Publicly available datasets were analyzed in this study. These data can be found at: <ext-link ext-link-type="uri" xlink:href="https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/">https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/</ext-link>.</p>
</sec>
<sec id="sec18">
<title>Author Contributions</title>
<p>ZZ and YT conceived and designed the research and wrote the paper. YT performed the experiments. YT, SZ, XL, and ZZ analyzed the data. All the authors have read and approved the final version of the manuscript. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="sec41" sec-type="funding-information">
<title>Funding</title>
<p>his study was supported by the National Natural Science Foundation of China (grant number 31772344) to ZZ. It is further supported by the Science and Technology Program of Beijing Municipality (grant number Z181100002518002). The funders played no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</p>
</sec>
<sec id="conf1" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The 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 id="sec001" sec-type="disclaimer">
<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 id="sec20" sec-type="supplementary-material">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link xlink:href="https://www.frontiersin.org/articles/10.3389/fpls.2021.738880/full#supplementary-material" ext-link-type="uri">https://www.frontiersin.org/articles/10.3389/fpls.2021.738880/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Table_1.docx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document" xmlns:xlink="http://www.w3.org/1999/xlink"/>
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</ref-list>
<glossary>
<def-list>
<title>Abbreviations</title>
<def-item>
<term>hpi</term>
<def>
<p>hours post inoculation</p>
</def>
</def-item>
<def-item>
<term>ML</term>
<def>
<p>maximum likelihood</p>
</def>
</def-item>
<def-item>
<term>RPKM</term>
<def>
<p>number of reads per kb per million reads</p>
</def>
</def-item>
<def-item>
<term>HMM</term>
<def>
<p>hidden Markov model</p>
</def>
</def-item>
<def-item>
<term>CWI</term>
<def>
<p>cell wall integrity</p>
</def>
</def-item>
<def-item>
<term>aa</term>
<def>
<p>amino acids</p>
</def>
</def-item>
<def-item>
<term>VIGS</term>
<def>
<p>virus-induced gene silencing</p>
</def>
</def-item>
</def-list>
</glossary>
<fn-group>
<fn id="fn0001"><p><sup>1</sup><ext-link xlink:href="http://pfam.xfam.org" ext-link-type="uri">http://pfam.xfam.org</ext-link></p></fn>
<fn id="fn0002"><p><sup>2</sup><ext-link xlink:href="https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/" ext-link-type="uri">https://lipm-browsers.toulouse.inra.fr/pub/RchiOBHm-V2/</ext-link></p></fn>
</fn-group>
</back>
</article>