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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.2022.1075199</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>Male-killing mechanisms vary between <italic>Spiroplasma</italic> species</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" corresp="yes">
<name><surname>Arai</surname> <given-names>Hiroshi</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>&#x002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1156896/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Inoue</surname> <given-names>Maki N.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/1158139/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Kageyama</surname> <given-names>Daisuke</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="corresp" rid="c002"><sup>&#x002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/612019/overview"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology</institution>, <addr-line>Fuchu</addr-line>, <country>Japan</country></aff>
<aff id="aff2"><sup>2</sup><institution>Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)</institution>, <addr-line>Tsukuba</addr-line>, <country>Japan</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Chih-Horng Kuo, Academia Sinica, Taiwan</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Steve Perlman, University of Victoria, Canada; Matt Ballinger, Mississippi State University, United States</p></fn>
<corresp id="c001">&#x002A;Correspondence: Hiroshi Arai, <email>dazai39papilio@gmail.com</email></corresp>
<corresp id="c002">Daisuke Kageyama, <email>kagymad@affrc.go.jp</email></corresp>
<fn fn-type="other" id="fn004"><p>This article was submitted to Microbial Symbioses, a section of the journal Frontiers in Microbiology</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>28</day>
<month>11</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>13</volume>
<elocation-id>1075199</elocation-id>
<history>
<date date-type="received">
<day>20</day>
<month>10</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>08</day>
<month>11</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2022 Arai, Inoue and Kageyama.</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Arai, Inoue and Kageyama</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>Male-killing, a male-specific death of arthropod hosts during development, is induced by <italic>Spiroplasma</italic> (Mollicutes) endosymbionts of the Citri&#x2013;Poulsonii and the Ixodetis groups, which are phylogenetically distant groups. <italic>Spiroplasma poulsonii</italic> induces male-killing in <italic>Drosophila melanogaster</italic> (Diptera) using the Spaid toxin that harbors ankyrin repeats, whereas little is known about the origin and mechanisms of male-killing induced by <italic>Spiroplasma ixodetis.</italic> Here, we analyzed the genome and the biological characteristics of a male-killing <italic>S. ixodetis</italic> strain <italic>s</italic>Hm in the moth <italic>Homona magnanima</italic> (Tortricidae, Lepidoptera). Strain <italic>s</italic>Hm harbored a 2.1 Mb chromosome and two potential plasmids encoding Type IV effectors, putatively involved in virulence and host&#x2013;symbiont interactions. Moreover, <italic>s</italic>Hm did not harbor the <italic>spaid</italic> gene but harbored 10 ankyrin genes that were homologous to those in other <italic>S. ixodetis</italic> strains. In contrast to the predominant existence of <italic>S. poulsonii</italic> in hemolymph, our quantitative PCR assays revealed a systemic distribution of strain <italic>s</italic>Hm in <italic>H. magnanima</italic>, with particularly high titers in Malpighian tubules but low titers in hemolymph. Furthermore, transinfection assays confirmed that strain <italic>s</italic>Hm can infect cultured cells derived from distantly related insects, namely <italic>Aedes albopictus</italic> (Diptera) and <italic>Bombyx mori</italic> (Lepidoptera). These results suggest different origins and characteristics of <italic>S. ixodetis</italic>- and <italic>S. poulsonii</italic>-induced male-killing.</p>
</abstract>
<kwd-group>
<kwd><italic>Spiroplasma</italic></kwd>
<kwd>male-killing</kwd>
<kwd>symbiosis</kwd>
<kwd>evolution</kwd>
<kwd>endosymbionts</kwd>
<kwd><italic>Homona magnanima</italic></kwd>
<kwd><italic>spaid</italic></kwd>
</kwd-group>
<contract-sponsor id="cn001">Japan Society for the Promotion of Science<named-content content-type="fundref-id">10.13039/501100001691</named-content></contract-sponsor><contract-sponsor id="cn002">Japan Society for the Promotion of Science<named-content content-type="fundref-id">10.13039/501100001691</named-content></contract-sponsor><contract-sponsor id="cn003">Japan Society for the Promotion of Science<named-content content-type="fundref-id">10.13039/501100001691</named-content></contract-sponsor>
<counts>
<fig-count count="6"/>
<table-count count="4"/>
<equation-count count="0"/>
<ref-count count="88"/>
<page-count count="15"/>
<word-count count="9506"/>
</counts>
</article-meta>
</front>
<body>
<sec id="S1" sec-type="intro">
<title>Introduction</title>
<p>In arthropods, maternally inherited endosymbiotic microbes frequently interact with the hosts in a mutualistic or a parasitic manner. Male-killing (MK), male-specific death in insects during development, is one of the reproductive manipulations induced by various intracellular bacteria, microsporidia, and viruses (<xref ref-type="bibr" rid="B22">Duron et al., 2008</xref>; <xref ref-type="bibr" rid="B81">Werren et al., 2008</xref>; <xref ref-type="bibr" rid="B43">Kageyama et al., 2012</xref>; <xref ref-type="bibr" rid="B26">Fujita et al., 2021</xref>). MK leads to the advantage of female siblings and is considered a selfish strategy of the intracellular microbes that promotes their spread and survival in nature (<xref ref-type="bibr" rid="B39">Hurst, 1991</xref>; <xref ref-type="bibr" rid="B38">Hurst and Jiggins, 2000</xref>; <xref ref-type="bibr" rid="B36">Hornett et al., 2006</xref>). The genus <italic>Spiroplasma</italic> (class: Mollicutes) are the most studied bacteria that induce MK in diverse insects (<xref ref-type="bibr" rid="B3">Anbutsu and Fukatsu, 2011</xref>; <xref ref-type="bibr" rid="B52">Lo et al., 2015</xref>; <xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>; <xref ref-type="bibr" rid="B14">Binetruy et al., 2019</xref>). <italic>Spiroplasma</italic> are small, helical, and motile bacteria that include commensal, pathogenic, and mutualistic species and have a diverse host range, including plants and animals (<xref ref-type="bibr" rid="B65">Regassa and Gasparich, 2006</xref>; <xref ref-type="bibr" rid="B20">Duperron et al., 2013</xref>; <xref ref-type="bibr" rid="B77">Viver et al., 2017</xref>; <xref ref-type="bibr" rid="B35">He et al., 2018</xref>). Phylogenetically, the MK <italic>Spiroplasma</italic> strains are clustered into the Citri&#x2013;Poulsonii group (harbored by <italic>Drosophila</italic> flies and lacewings) (<xref ref-type="bibr" rid="B84">Williamson and Poulson, 1979</xref>; <xref ref-type="bibr" rid="B34">Hayashi et al., 2016</xref>) and the Ixodetis clade (harbored by ladybugs, butterflies, moths, and aphids) (<xref ref-type="bibr" rid="B37">Hurst et al., 1999</xref>; <xref ref-type="bibr" rid="B67">Simon et al., 2011</xref>; <xref ref-type="bibr" rid="B69">Tabata et al., 2011</xref>; <xref ref-type="bibr" rid="B68">Smith et al., 2016</xref>).</p>
<p>The molecular mechanisms underlying <italic>Spiroplasma</italic>-induced MK have been mostly investigated using <italic>S. poulsonii</italic>&#x2013;<italic>Drosophila</italic> systems (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>). <italic>S. poulsonii</italic> strain MSRO induces MK in <italic>Drosophila melanogaster</italic> by a toxic protein androcidin (Spaid) harboring ankyrin repeats that damage the male X chromosome (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>). In contrast, information regarding the mechanism underlying MK induced by the members of the Ixodetis group is limited. The <italic>spaid</italic> gene is conserved among <italic>S. poulsonii</italic> strains (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>; <xref ref-type="bibr" rid="B28">Gerth et al., 2021</xref>), whereas whether the <italic>S. ixodetis</italic> group uses Spaid as an MK factor is unknown. The genus <italic>Spiroplasma</italic> exhibits high genomic flexibility and dynamic evolution of various toxin loci, such as Spaid and ribosome-inactivating protein (RIP) (<xref ref-type="bibr" rid="B31">Hamilton et al., 2016</xref>; <xref ref-type="bibr" rid="B12">Ballinger et al., 2019</xref>; <xref ref-type="bibr" rid="B28">Gerth et al., 2021</xref>; <xref ref-type="bibr" rid="B55">Massey and Newton, 2022</xref>; <xref ref-type="bibr" rid="B63">Pollmann et al., 2022</xref>). Gnomic analyses have revealed dynamic <italic>Spiroplasma</italic> evolution driven by bacteriophage lysogenization (<xref ref-type="bibr" rid="B85">Ye et al., 1996</xref>; <xref ref-type="bibr" rid="B18">Carle et al., 2010</xref>; <xref ref-type="bibr" rid="B46">Ku et al., 2013</xref>) and by horizontal gene transfer (<xref ref-type="bibr" rid="B58">Mouches et al., 1984</xref>; <xref ref-type="bibr" rid="B41">Joshi et al., 2005</xref>). Virulence-associated genes are frequently exchanged between microbes sharing the same niche (<xref ref-type="bibr" rid="B44">Kent and Bordenstein, 2010</xref>; <xref ref-type="bibr" rid="B83">Wiedenbeck and Cohan, 2011</xref>). Likewise, <italic>Spiroplasma</italic> may have acquired MK genes by horizontal gene transfer because they often coexist with other endosymbionts, such as <italic>Wolbachia</italic> and <italic>Rickettsia</italic>, in the same host (<xref ref-type="bibr" rid="B37">Hurst et al., 1999</xref>; <xref ref-type="bibr" rid="B53">Majerus et al., 2000</xref>; <xref ref-type="bibr" rid="B80">Watanabe et al., 2012</xref>; <xref ref-type="bibr" rid="B34">Hayashi et al., 2016</xref>; <xref ref-type="bibr" rid="B71">Takamatsu et al., 2021</xref>). However, the horizontal gene transfer to <italic>Spiroplasma</italic> may be constrained by the unusual codon usage by <italic>Spiroplasma</italic> compared with other bacteria (notably, the use of UGA as a tryptophan rather than a stop codon; <xref ref-type="bibr" rid="B52">Lo et al., 2015</xref>). Although genomic studies on MK <italic>S. poulsonii</italic> have been done, comparative genomic analyses of other MK <italic>Spiroplasma</italic> species, such as <italic>S. ixodetis</italic>, are essential to infer the origin and evolution of the MK machinery.</p>
<p>In this study, we sequenced the genome of <italic>S. ixodetis</italic> strain <italic>s</italic>Hm that causes MK in the tea tortrix moth <italic>Homona magnanima</italic> (Tortricidae, Lepidoptera). Against the full-genome sequence of strain <italic>s</italic>Hm, we searched for genes encoding Spaid and RIP toxin homologs, as well as putative MK genes of other MK endosymbionts such as <italic>Wolbachia</italic> (<xref ref-type="bibr" rid="B8">Arai et al., 2020</xref>, <xref ref-type="bibr" rid="B4">2022a</xref>) and Partiti-like virus Osugoroshivirus (OGVs) (<xref ref-type="bibr" rid="B26">Fujita et al., 2021</xref>) in <italic>H. magnanima</italic>. We also examined the propagation characteristics and infectivity of strain <italic>s</italic>Hm using quantification and transinfection assays. Finally, we argue that MK mechanisms and ecological characteristics are substantially different between <italic>Spiroplasma</italic> species.</p>
</sec>
<sec id="S2" sec-type="materials|methods">
<title>Materials and methods</title>
<sec id="S2.SS1">
<title>Rearing and sexing of <italic>Homona magnanima</italic></title>
<p>To construct <italic>S. ixodetis</italic> sHm genome, we used the laboratory-maintained <italic>Spiroplasma</italic>-positive MK-inducing line (S+ line) of <italic>H. magnanima</italic> (<xref ref-type="bibr" rid="B75">Tsugeno et al., 2017</xref>). In the present study, we accidentally obtained a <italic>Spiroplasma</italic>-positive 1:1 sex ratio line (S+M+ line) as a subline of the S+ line. For every generation, the male moths picked up from the 1:1 sex ratio line, which had been confirmed negative for <italic>Spiroplasma</italic>, <italic>Wolbachia</italic>, and OGV (NSR line) (<xref ref-type="bibr" rid="B71">Takamatsu et al., 2021</xref>), were crossed with the female moths of the S+ and S+M+ lines as described by <xref ref-type="bibr" rid="B4">Arai et al. (2022a)</xref>. The obtained larvae were reared using artificial diet SilkMate 2S (Nosan Co., Yokohama, Japan) at 25&#x00B0;C under a long photoperiod (16L:8D), i.e., till pupation. To eliminate <italic>Spiroplasma</italic> from the S+ line, the first instar larvae were reared with SilkMate 2S supplemented with 0.05% tetracycline (w/w) as described by <xref ref-type="bibr" rid="B7">Arai et al. (2019)</xref>. Adult moths were sexed based on their morphology, and the hatched larvae and the unhatched pharate larvae (mature embryo) were sexed based on the presence or absence of the female-specific sex chromatin body (a condensed W chromosome), which was detected <italic>via</italic> lactic-acetic orcein staining (<xref ref-type="bibr" rid="B4">Arai et al., 2022a</xref>).</p>
</sec>
<sec id="S2.SS2">
<title><italic>Spiroplasma</italic> detection and quantification in <italic>Homona magnanima</italic></title>
<p>Total DNA was extracted from the abdomen of female adults (0-day post eclosion), the whole body of larvae and pupae (0-day post molting), and dissected tissues of <italic>H. magnanima</italic> larvae (0-day post molting) using cell lysis buffer, as described by <xref ref-type="bibr" rid="B7">Arai et al. (2019)</xref>. To detect <italic>Spiroplasma</italic>, a pair of <italic>Spiroplasma</italic>-specific primers was used to amplify RNA polymerase &#x03B2; subunit gene (<italic>RpoB</italic>), which is a single copy conserved gene in <italic>Spiroplasma</italic> spp., from the extracted DNA (adjusted to 50&#x2013;100 ng/reaction) with EmeraldAmp MAX PCR Master Mix (TaKaRa Bio, Shiga, Japan); the primer sets are listed in <xref ref-type="table" rid="T1">Table 1</xref>. The PCR conditions were as follows: 35 cycles of 94&#x00B0;C for 30 s, 55&#x00B0;C for 30 s, and 72&#x00B0;C for 30 s, followed by 72&#x00B0;C for 7 min. &#x03B2;-Actin gene of <italic>H. magnanima</italic> was used as the control. To quantify <italic>Spiroplasma</italic> density, qPCR was performed using the extracted DNA, which was diluted to a concentration of 10 ng/&#x03BC;L with MilliQ water, <italic>Spiroplasma RpoB</italic> primers (<xref ref-type="table" rid="T1">Table 1</xref>), and KOD SYBR<sup>&#x00AE;</sup> qPCR Mix (Toyobo, Osaka, Japan) in a LightCycler<sup>&#x00AE;</sup> 96 system (Roche, Basel, Switzerland). The PCR consisted of 45 cycles of 98&#x00B0;C for 10 s, 60&#x00B0;C for 10 s, and 68&#x00B0;C for 30 s. Relative abundance of the gene was calculated using the expression of elongation factor 1a gene (<italic>ef1a</italic>) of <italic>H. magnanima</italic> as the control. <italic>Spiroplasma</italic> density (<italic>RpoB</italic> copies) and relative abundance (<italic>RpoB</italic>/<italic>ef1a</italic>) were calculated as described in <xref ref-type="bibr" rid="B7">Arai et al. (2019</xref>, <xref ref-type="bibr" rid="B6">2022c)</xref>.</p>
<table-wrap position="float" id="T1">
<label>TABLE 1</label>
<caption><p>Sequences and related information of the primers used in this study.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Target</td>
<td valign="top" align="left">Gene</td>
<td valign="top" align="left">Primers sequences (5&#x2032;&#x2013;3&#x2032;)</td>
<td valign="top" align="center">Product size (bp)</td>
<td valign="top" align="center">Annealing temperature (&#x00B0;C)</td>
<td valign="top" align="left">References</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><italic>H. magnanima</italic></td>
<td valign="top" align="left">&#x03B2;-Actin</td>
<td valign="top" align="left">297f:AACTGGGATGACATGGAGAAGATCTGGC</td>
<td valign="top" align="center">838</td>
<td valign="top" align="center">55</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B75">Tsugeno et al., 2017</xref></td>
</tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">1139r: GAGATCCACATCTGCTGGAAGGTGGACAG</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
<tr>
<td/>
<td valign="top" align="left"><italic>HmEf-1a</italic></td>
<td valign="top" align="left">Hmef1a_F_val1_85: TTTCCAGGGTGGTTGAGCA</td>
<td valign="top" align="center">108</td>
<td valign="top" align="center">60</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B6">Arai et al., 2022c</xref></td>
</tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">Hmef1a_R_val1_193: CCGTTAAGGAGCTGCGTCG</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
<tr>
<td/>
<td valign="top" align="left"><italic>COI</italic></td>
<td valign="top" align="left">LepF: ATTCAACCAATCATAAAGATATTGG</td>
<td valign="top" align="center">650</td>
<td valign="top" align="center">55</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B30">Hajibabaei et al., 2006</xref></td>
</tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">LepR: TAAACTTCTGGATGTCCAAAAAATCA</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left"><italic>Spiroplasma</italic></td>
<td valign="top" align="left"><italic>RpoB</italic></td>
<td valign="top" align="left">HmSpiro_RpoB388qF: GCATACTCAACACCCGTACCA</td>
<td valign="top" align="center">95</td>
<td valign="top" align="center">60</td>
<td valign="top" align="left">This study</td>
</tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">HmSpiro_RpoB483qR: TGCTAACCGTGCTTTAATGGG</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">HmSpiro_RpoB155F: CGCCATCTTTCATCGAAGGTC</td>
<td valign="top" align="center">423</td>
<td valign="top" align="center">60</td>
<td valign="top" align="left"/></tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">HmSpiro_RpoB578R ATTGTTGGACCAAACGAAGTTG</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
</tbody>
</table></table-wrap>
</sec>
<sec id="S2.SS3">
<title>Genome sequence of the <italic>Spiroplasma</italic> sHm strain</title>
<p>For genome sequencing of strain <italic>s</italic>Hm, high molecular weight DNA was extracted from the egg masses of S+ line moths using Nanobind Tissue Big DNA Kit (Circulomics Inc., MD, USA) and used for library construction using Ultra-Long DNA Sequencing Kit (Oxford Nanopore Technologies, Oxford, UK) following the manufacture&#x2019;s protocol. The constructed libraries were sequenced using ONT MinION flow cell (R 9.4.1) (Oxford Nanopore Technologies). The obtained reads were mapped to the <italic>H. magnanima</italic> reference genome (Jouraku et al., in preparation) with minimap2 (<xref ref-type="bibr" rid="B49">Li, 2018</xref>), and the non-mapped reads containing <italic>Spiroplasma</italic> reads were extracted with SAMtools v.1.9 (<xref ref-type="bibr" rid="B50">Li et al., 2009</xref>) and assembled using Canu 1.6 (<xref ref-type="bibr" rid="B45">Koren et al., 2017</xref>). The draft <italic>Spiroplasma</italic> genome (a circular main chromosome and plasmids) was annotated <italic>via</italic> BLASTn (NCBI nr database). The extracted DNA was also subjected to Illumina paired-end 150 bp sequencing (PE-150) at Novogene (Beijing, China). The Illumina data were used to polish the draft genome using minimap2 (<xref ref-type="bibr" rid="B49">Li, 2018</xref>) and Pilon v. 1.23 (<xref ref-type="bibr" rid="B79">Walker et al., 2014</xref>). Since no sequence changes were observed after the second polishing, the polished genome was considered as the complete genome of strain <italic>s</italic>Hm. The circularity of the <italic>s</italic>Hm genome was confirmed by BLASTn search, followed by manual deletion of overlapping sequence.</p>
</sec>
<sec id="S2.SS4">
<title>Resequencing of the sHm strain in the S+ and S+M+ moth lines</title>
<p>S+ (MK line) and S+M+ <italic>H. magnanima</italic> lines (non-MK line) were used for DNA extraction as described by <xref ref-type="bibr" rid="B4">Arai et al. (2022a)</xref>. The DNA extracted from <italic>Spiroplasma</italic> cells was amplified using whole genome amplification (WGA) by REPLI-g Mini Kit (Qiagen, Hilden, Germany), following the manufacture&#x2019;s protocol. The WGA products, purified using AMPure XP beads (Beckman Coulter, Inc., CA, USA) and dissolved into TE buffer, were sequenced on Illumina platform (PE-150). The Illumina data assembled with unicycler (<xref ref-type="bibr" rid="B82">Wick et al., 2017</xref>) and Illumina raw read data were mapped to the <italic>s</italic>Hm reference genome using minimap2 (<xref ref-type="bibr" rid="B49">Li, 2018</xref>) to detect the genomic changes in the genome of <italic>s</italic>Hm in the S + M + line.</p>
</sec>
<sec id="S2.SS5">
<title>Genome annotations and homology surveys</title>
<p>The constructed <italic>s</italic>Hm genome was annotated <italic>via</italic> DFAST (<xref ref-type="bibr" rid="B72">Tanizawa et al., 2018</xref>). Effector genes were further annotated using EffectiveDB (<xref ref-type="bibr" rid="B23">Eichinger et al., 2016</xref>). Functional analysis of proteins (i.e., domain predictions and Gene ontology annotations) was conducted using InterPro.<sup><xref ref-type="fn" rid="footnote1">1</xref></sup> Phage WO infections were annotated using PHASTER (<xref ref-type="bibr" rid="B9">Arndt et al., 2016</xref>). Protein homology between different <italic>Spiroplasma</italic> strains was analyzed using <italic>S. apis</italic> B31 (CP006682.1), <italic>S. citri</italic> strain BLH-MB (CP047437.1&#x2013;CP047446.1), <italic>S. syrphidicola</italic> strain EA-1 (NC_021284.1), <italic>D. melanogaster</italic> endosymbiont <italic>S. poulsonii</italic> MSRO (CM020866.1&#x2013;CM020867.1) (<italic>s</italic>Mel, MK strain, <xref ref-type="bibr" rid="B56">Masson et al., 2018</xref>), <italic>Danaus chrysippus</italic> (Nymphalidae) endosymbiont <italic>S. ixodetis</italic> (NZ_CADDIL010000001.1&#x2013;NZ_CADDIL010000012.1) (<italic>s</italic>Da, MK strain, <xref ref-type="bibr" rid="B54">Martin et al., 2020</xref>), <italic>Lariophagus distinguendus</italic> (Pteromalidae) endosymbiont <italic>S. ixodetis</italic> (NZ_JALMUW010000001.1&#x2013;NZ_JALMUW010000198.1) [<italic>s</italic>Dis, cytoplasmic incompatibility (CI) strain, <xref ref-type="bibr" rid="B63">Pollmann et al., 2022</xref>], and <italic>Dactylopius coccus</italic> (Dactylopiidae) endosymbiont <italic>S. ixodetis</italic> (JACSER010000001.1&#x2013;JACSER010000358.1) (<italic>s</italic>Coc, non-MK strain, <xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al., 2021</xref>) with OrthoVenn2.<sup><xref ref-type="fn" rid="footnote2">2</xref></sup> Homology of <italic>s</italic>Hm genes and proteins with <italic>spaid</italic> from strain <italic>s</italic>Mel (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>), ankyrin genes from <italic>S. ixodetis</italic> (<xref ref-type="bibr" rid="B86">Yeoman et al., 2019</xref>; <xref ref-type="bibr" rid="B54">Martin et al., 2020</xref>; <xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al., 2021</xref>), and the <italic>Wolbachia</italic> MK candidate factor responsible for WO-mediated killing (Wmk, presumed helix-turn-helix transcriptional regulator, <xref ref-type="bibr" rid="B60">Perlmutter et al., 2019</xref>; <xref ref-type="bibr" rid="B5">Arai et al., 2022b</xref>) was evaluated using both BLASTn and BLASTp. Moreover, to verify whether MK microbes of <italic>H. magnanima</italic> carried conserved genes, the genes on the MK-associated prophage region WO<italic>w</italic>Hm-t76 of MK <italic>Wolbachia w</italic>Hm-t (<xref ref-type="bibr" rid="B5">Arai et al., 2022b</xref>) and those of the Partiti-like virus OGVs (<xref ref-type="bibr" rid="B26">Fujita et al., 2021</xref>) were compared to the <italic>s</italic>Hm genes using both BLASTn and BLASTp. Unique genomic features of the <italic>s</italic>Hm strain in the MK S+ and non-MK S+M+ <italic>H. magnanima</italic> lines were analyzed using GView<sup><xref ref-type="fn" rid="footnote3">3</xref></sup> and BV-BRC variation analysis service.<sup><xref ref-type="fn" rid="footnote4">4</xref></sup> Metabolic pathways of <italic>S. poulsonii s</italic>Mel and <italic>S. ixodetis s</italic>Hm were compared by using BV-BRC comparative analysis service (see text footnote 4). Phylogenetic trees of 16S rRNA gene and ankyrin genes of <italic>Spiroplasma</italic> strains were constructed by maximum likelihood with bootstrap re-sampling of 1,000 replicates using MEGA7 (<xref ref-type="bibr" rid="B47">Kumar et al., 2016</xref>). <italic>Mycoplasma genitalium</italic> G-37 (NR074611.1) was used as an outgroup.</p>
</sec>
<sec id="S2.SS6">
<title>Transinfection assays</title>
<p>A fifth instar female larva was sterilized in 50% bleach (ca. 3% sodium hypochlorite) for 10 min, in 70% ethanol for 10 min, and dissected in IPL-41 Insect Medium (Gibco, Carlsbad, CA, USA) supplemented with 10% (v/v) fetal bovine serum (FBS). Malpighian tubules of the dissected larva were transferred to flasks containing either the <italic>Bombyx mori</italic> NIAS-Bm-aff3 (aff3) cell line (<xref ref-type="bibr" rid="B70">Takahashi et al., 2006</xref>) or the <italic>Aedes albopictus</italic> NIAS-AeAl-2 (AeAl2) cell line (<xref ref-type="bibr" rid="B57">Mitsuhashi, 1981</xref>) maintained in IPL-41 Insect Medium (Gibco) with 10% (v/v) of FBS. The cells and Malpighian tubules were co-cultured at 23&#x00B0;C. Fresh medium was supplied to the flask every 10 d. Purified cells centrifuged at 1,000 <italic>g</italic> for 2 min were used to analyze infections and titers of the transinfected strain <italic>s</italic>Hm in the cells. DNA extraction, PCR, and qPCR assays were performed as mentioned in section &#x201C;Spiroplasma detection and quantification in <italic>Homona magnanima</italic>.&#x201D;</p>
</sec>
<sec id="S2.SS7">
<title>Statistical analysis</title>
<p>Sex ratio bias was assessed using Fisher&#x2019;s exact test. <italic>Spiroplasma</italic> densities, male ratio in hatched larvae, and male ratio in unhatched pharate larvae were analyzed using either the Wilcoxon test or the Steel--Dwass test. All analyses were performed using R software v4.0<sup><xref ref-type="fn" rid="footnote5">5</xref></sup>.</p>
</sec>
</sec>
<sec id="S3" sec-type="results|discussion">
<title>Results and discussion</title>
<sec id="S3.SS1">
<title><italic>Spiroplasma ixodetis</italic> strain sHm induced embryonic male death in <italic>Homona magnanima</italic></title>
<p>The S+ line moths harboring <italic>s</italic>Hm exhibited lower egg-hatching rates than the NSR line (<xref ref-type="fig" rid="F1">Figure 1A</xref>), which is consistent with the results from previous studies that <italic>Spiroplasma</italic> infection halved the egg hatching rates of <italic>H. magnanima</italic> (<xref ref-type="bibr" rid="B75">Tsugeno et al., 2017</xref>; <xref ref-type="bibr" rid="B71">Takamatsu et al., 2021</xref>). Cytogenetic sexing based on the presence or absence of a sex chromatin body (W chromosome) revealed that the sex ratio of hatched larvae was strongly biased toward females in the S+ line moths but not in the NSR line moths (<italic>P</italic> &#x003C; 0.01, <xref ref-type="fig" rid="F1">Figure 1B</xref>). In contrast, the sex ratio of unhatched pharate larvae (late-stage embryos) were male-biased in the <italic>s</italic>Hm-infected line (S+) (Fisher&#x2019;s exact test, <italic>P</italic> &#x003C; 0.01), confirming that <italic>s</italic>Hm killed male <italic>H. magnanima</italic> during embryogenesis. Moreover, the elimination of <italic>Spiroplasma</italic> by tetracycline treatment resulted in non-biased sex ratios in the subsequent generation (<italic>P</italic> &#x003C; 0.01, <xref ref-type="fig" rid="F1">Figure 1C</xref>).</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption><p>Egg hatching rates and sex ratios of the S+ line of <italic>Homona magnanima.</italic> <bold>(A)</bold> Egg hatching rates of 25 egg masses for each of the NSR and S+ lines (total 3,645 and 3,322 eggs, respectively). <bold>(B)</bold> Proportion of males among the hatched larvae and the unhatched pharate larvae. <bold>(C)</bold> Proportion of males of the subsequent generation after tetracycline treatment. Tet, tetracycline treatment; Control, non-treated control. The horizontal bar within the box represents the median. The upper and lower hinges of the box indicate upper quartile and lower quartile, respectively. Sample sizes are indicated below the panels. Different letters indicate significant differences between groups (Steel&#x2013;Dwass test, <italic>P</italic> &#x003C; 0.05).</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-13-1075199-g001.tif"/>
</fig>
</sec>
<sec id="S3.SS2">
<title>Genome sequence and genetic characteristics of male-killing <italic>Spiroplasma ixodetis</italic> strain sHm</title>
<p>Both Illumina (816.3 Mb, 5,442,459 reads, and 150 bp average length) and Nanopore data (93.5 Mb, 25,820 reads, and 3,624 bp average length) were used to reconstruct a complete genome consisting of a circular main chromosome (2, 102,039 bp in length) and two circular potential plasmids [20,119 bp (pSHM_1) and 16,408 bp (pSHM_2)]. Previously, <xref ref-type="bibr" rid="B75">Tsugeno et al. (2017)</xref> reported two 16S rRNA gene variants cloned from <italic>Spiroplasma</italic>-infected <italic>H. magnanima</italic>, but they did not elucidate whether the two sequences were interoperonic polymorphs of a single isolate or they were derived from two different strains. The present study confirmed that <italic>H. magnanima</italic> was infected with the MK <italic>S. ixodetis</italic> strain <italic>s</italic>Hm that harbored two distinct 16S rRNA gene sequences in its genome (<xref ref-type="fig" rid="F2">Figure 2</xref>). Moreover, <italic>Spiroplasma</italic> strains often encode multiple ribosomal RNA gene sets in their genome (<xref ref-type="bibr" rid="B19">Chang et al., 2014</xref>; <xref ref-type="bibr" rid="B74">Tsai et al., 2018</xref>; <xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al., 2021</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption><p>Phylogenetic tree of <italic>Spiroplasma</italic> strains based on 16S rRNA gene sequences. Phylogenetic tree based on 16S rRNA gene sequences of strain <italic>s</italic>Hm and other <italic>Spiroplasma</italic> strains (retrieved from NCBI database) using maximum likelihood method based on the Tamura&#x2013;Nei model with 1,000 bootstrap replicates. Accession numbers are shown along with the operational taxonomic units (OTUs). Samples highlighted with red and blue color fonts are MK and CI strains, respectively. Black diamonds indicate 16S rRNA sequences of the <italic>s</italic>Hm. The classification of <italic>Spiroplasma</italic> is based on the study by <xref ref-type="bibr" rid="B59">Paredes et al. (2015)</xref>. <italic>Mycoplasma genitalium</italic> was used as the outgroup.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fmicb-13-1075199-g002.tif"/>
</fig>
<p>Strain <italic>s</italic>Hm harbored a higher number of coding sequences (CDS; 2,886 CDS) than strains <italic>s</italic>Mel (1.9 Mb in genome size; 2,405 CDS; <xref ref-type="bibr" rid="B56">Masson et al., 2018</xref>) and <italic>s</italic>Da (1.7 Mb in genome size; 1,813 CDS; <xref ref-type="bibr" rid="B54">Martin et al., 2020</xref>; <xref ref-type="table" rid="T2">Table 2</xref>). Although plasmids often contain key accessory genes such as <italic>spaid</italic> of <italic>s</italic>Mel (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>), genes on pSHM_1 (<italic>n</italic> = 24) and pSHM_2 (<italic>n</italic> = 20) mostly encoded hypothetical or uncharacterized proteins (<xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>). In addition, strain <italic>s</italic>Hm harbored 12 prophage regions (size: 6.6&#x2013;14.8 kb) in its genome, which is consistent with previous reports that several phage sequences are found in <italic>Spiroplasma</italic> genomes (<xref ref-type="bibr" rid="B10">Bai and Hogenhout, 2002</xref>; <xref ref-type="bibr" rid="B51">Lo et al., 2013</xref>; <xref ref-type="bibr" rid="B64">Ramirez et al., 2021</xref>). Bacteriophages frequently carry virulence-associated genes that encode toxins (<xref ref-type="bibr" rid="B78">Waldor and Mekalanos, 1996</xref>; <xref ref-type="bibr" rid="B17">Br&#x00FC;ssow et al., 2004</xref>). Recently, the mechanistic bases of <italic>Wolbachia</italic>-induced cytoplasmic incompatibility (CI) and MK have been attributed to phages (<xref ref-type="bibr" rid="B13">Beckmann et al., 2017</xref>; <xref ref-type="bibr" rid="B48">LePage et al., 2017</xref>; <xref ref-type="bibr" rid="B60">Perlmutter et al., 2019</xref>; <xref ref-type="bibr" rid="B5">Arai et al., 2022b</xref>). Besides, phages have also been implicated in the defense phenotype exhibited by bacteria against parasitoids, such as <italic>Hamiltonella defensa</italic> (<xref ref-type="bibr" rid="B16">Brandt et al., 2017</xref>). Therefore, it is possible that the phages of <italic>s</italic>Hm contribute to the manifestation of MK phenotype or confer fitness advantage on hosts by protecting the hosts from natural enemies.</p>
<table-wrap position="float" id="T2">
<label>TABLE 2</label>
<caption><p>Genomic features of strain <italic>s</italic>Hm and other <italic>Spiroplasma</italic> strains found in insects.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left">Genome ID</td>
<td valign="top" align="left"><italic>Spiroplasma ixodetis s</italic>Hm</td>
<td valign="top" align="left"><italic>Spiroplasma ixodetis s</italic>Da</td>
<td valign="top" align="left"><italic>Spiroplasma ixodetis</italic> DCM</td>
<td valign="top" align="left"><italic>Spiroplasma ixodetis s</italic>Dis</td>
<td valign="top" align="left"><italic>Spiroplasma poulsonii</italic> MSRO</td>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Main chromosome/contigs</td>
<td valign="top" align="left">1 (closed/circular)</td>
<td valign="top" align="left">12</td>
<td valign="top" align="left">353</td>
<td valign="top" align="left">198</td>
<td valign="top" align="left">1 (closed/circular)</td>
</tr>
<tr>
<td valign="top" align="left">Plasmids</td>
<td valign="top" align="left">2 (closed/circular)</td>
<td valign="top" align="left">NA</td>
<td valign="top" align="left">NA</td>
<td valign="top" align="left">3 (closed/circular)</td>
<td valign="top" align="left">1 (closed/circular)</td>
</tr>
<tr>
<td valign="top" align="left">Estimated genome size (Mb)</td>
<td valign="top" align="left">2.14</td>
<td valign="top" align="left">1.75</td>
<td valign="top" align="left">1.32</td>
<td valign="top" align="left">1.16</td>
<td valign="top" align="left">1.96</td>
</tr>
<tr>
<td valign="top" align="left">N50</td>
<td valign="top" align="left">2,102,039</td>
<td valign="top" align="left">265,779</td>
<td valign="top" align="left">7,774</td>
<td valign="top" align="left">14,219</td>
<td valign="top" align="left">1,938,611</td>
</tr>
<tr>
<td valign="top" align="left">G + C content (%)</td>
<td valign="top" align="left">25.1</td>
<td valign="top" align="left">23.7</td>
<td valign="top" align="left">24.16</td>
<td valign="top" align="left">24.3</td>
<td valign="top" align="left">26.3</td>
</tr>
<tr>
<td valign="top" align="left">CDS genes</td>
<td valign="top" align="left">2,886</td>
<td valign="top" align="left">1,813</td>
<td valign="top" align="left">1,371</td>
<td valign="top" align="left">1,175</td>
<td valign="top" align="left">2,405</td>
</tr>
<tr>
<td valign="top" align="left">rRNA (16S, 5S, 23S)</td>
<td valign="top" align="left">6 (2,2,2)</td>
<td valign="top" align="left">4 (1,2,1)</td>
<td valign="top" align="left">3 (1,1,1)</td>
<td valign="top" align="left">3 (1,1,1)</td>
<td valign="top" align="left">3 (1,1,1)</td>
</tr>
<tr>
<td valign="top" align="left">tRNA</td>
<td valign="top" align="left">27</td>
<td valign="top" align="left">27</td>
<td valign="top" align="left">27</td>
<td valign="top" align="left">27</td>
<td valign="top" align="left">31</td>
</tr>
<tr>
<td valign="top" align="left">Phenotype</td>
<td valign="top" align="left">MK<xref ref-type="table-fn" rid="t2fn1"><sup>1</sup></xref></td>
<td valign="top" align="left">MK<xref ref-type="table-fn" rid="t2fn2"><sup>2</sup></xref></td>
<td valign="top" align="left">non-MK<xref ref-type="table-fn" rid="t2fn3"><sup>3</sup></xref></td>
<td valign="top" align="left">CI<xref ref-type="table-fn" rid="t2fn4"><sup>4</sup></xref></td>
<td valign="top" align="left">MK<xref ref-type="table-fn" rid="t2fn5"><sup>5</sup></xref></td>
</tr>
<tr>
<td valign="top" align="left">Insect associated</td>
<td valign="top" align="left"><italic>Homona magnanima</italic><xref ref-type="table-fn" rid="t2fn1"><sup>1</sup></xref></td>
<td valign="top" align="left"><italic>Danaus chrysippus</italic><xref ref-type="table-fn" rid="t2fn2"><sup>2</sup></xref></td>
<td valign="top" align="left"><italic>Dactylopius coccus</italic><xref ref-type="table-fn" rid="t2fn3"><sup>3</sup></xref></td>
<td valign="top" align="left"><italic>Lariophagus distinguendus</italic><xref ref-type="table-fn" rid="t2fn4"><sup>4</sup></xref></td>
<td valign="top" align="left"><italic>Drosophila melanogaster</italic><xref ref-type="table-fn" rid="t2fn5"><sup>5</sup></xref></td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn id="t2fn1"><p><sup>1</sup>Based on <xref ref-type="bibr" rid="B75">Tsugeno et al. (2017)</xref>.</p></fn>
<fn id="t2fn2"><p><sup>2</sup>Based on <xref ref-type="bibr" rid="B54">Martin et al. (2020)</xref>.</p></fn>
<fn id="t2fn3"><p><sup>3</sup>Based on <xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al. (2021)</xref>.</p></fn>
<fn id="t2fn4"><p><sup>4</sup>Based on <xref ref-type="bibr" rid="B63">Pollmann et al. (2022)</xref>.</p></fn>
<fn id="t2fn5"><p><sup>5</sup>Based on <xref ref-type="bibr" rid="B56">Masson et al. (2018)</xref>.</p></fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="S3.SS3">
<title>sHm harbored putative virulence-associated factors but did not harbor sMel spaid toxin</title>
<p>Recently, <xref ref-type="bibr" rid="B86">Yeoman et al. (2019)</xref> and <xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al. (2021)</xref> reported that <italic>D. coccus</italic>-infecting <italic>S. ixodetis</italic> (sCoc) harbored a <italic>spaid</italic> homolog and <italic>Cephus cinctus</italic> (Cephidae)-infecting <italic>S. ixodetis</italic> harbored seven <italic>spaid</italic> homologs. Our BLAST searches confirmed that <italic>s</italic>Hm did not harbor the <italic>spaid</italic> gene (<xref ref-type="table" rid="T3">Table 3</xref>), however, some of the ankyrin genes of <italic>s</italic>Hm were homologous to the alleged gene sequences of <italic>s</italic>Coc and Cephidae-infecting <italic>S. ixodetis</italic> (<xref ref-type="table" rid="T4">Table 4</xref>). It is likely that <italic>S. ixodetis</italic> do not harbor the <italic>spaid</italic> gene. The superficial homology could be due to the presence of conserved ankyrin repeats (<xref ref-type="table" rid="T3">Table 3</xref>). Similarly, the amino acid sequences of ankyrin proteins of <italic>s</italic>Hm (such as SHM_18920) showed partial homology to the ankyrin domain of Spaid from strain <italic>s</italic>Mel (N-terminal 200 amino acids) as per BLASTp search, but the complete amino acid sequences of the proteins of these two strains were not homologous (<xref ref-type="table" rid="T3">Table 3</xref>). Moreover, we also confirmed the absence of Spaid homologs in a MK <italic>S. ixodetis</italic> strain <italic>s</italic>Da by using BLASTp search. <xref ref-type="bibr" rid="B28">Gerth et al. (2021)</xref> reported that the Spaid homologs are conserved among <italic>S. poulsonii</italic> strains regardless of the MK phenotype. Because the spaid gene is not likely to be possessed by <italic>S. ixodetis</italic>, MK mechanisms may differ between <italic>S. poulsonii</italic> and <italic>S. ixodetis</italic> (i.e., having different causative genes).</p>
<table-wrap position="float" id="T3">
<label>TABLE 3</label>
<caption><p>Homology between Spaid [1,065 aa] of strain <italic>s</italic>Mel and proteins of <italic>Spiroplasma ixodetis</italic> strains based on BLASTp search.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left"><italic>Spiroplasma ixodetis</italic> proteins</td>
<td valign="top" align="center">Identity</td>
<td valign="top" align="center">Aligned length</td>
<td valign="top" align="center" colspan="2"><italic>s</italic>Mel spaid<hr/></td>
<td valign="top" align="center" colspan="2"><italic>Spiroplasma ixodetis</italic><hr/></td>
<td valign="top" align="center"><italic>e</italic>-value</td>
<td valign="top" align="center">Bit score</td>
<td valign="top" align="left">References</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left">Start</td>
<td valign="top" align="center">End</td>
<td valign="top" align="center">Start</td>
<td valign="top" align="center">End</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">sHm (SHM_18920)</td>
<td valign="top" align="center">36.0</td>
<td valign="top" align="center">205</td>
<td valign="top" align="center">217</td>
<td valign="top" align="center">409</td>
<td valign="top" align="center">60</td>
<td valign="top" align="center">261</td>
<td valign="top" align="center">2.99E-29</td>
<td valign="top" align="center">111</td>
<td valign="top" align="left">This study</td>
</tr>
<tr>
<td valign="top" align="left">sDa (SPD_05340)</td>
<td valign="top" align="center">40.9</td>
<td valign="top" align="center">220</td>
<td valign="top" align="center">54</td>
<td valign="top" align="center">266</td>
<td valign="top" align="center">28</td>
<td valign="top" align="center">237</td>
<td valign="top" align="center">5.56E-34</td>
<td valign="top" align="center">117</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B54">Martin et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">sCoc spaid-like (JACSEQ010000039.1)</td>
<td valign="top" align="center">48.7</td>
<td valign="top" align="center">80</td>
<td valign="top" align="center">137</td>
<td valign="top" align="center">216</td>
<td valign="top" align="center">21</td>
<td valign="top" align="center">100</td>
<td valign="top" align="center">5.71E-21</td>
<td valign="top" align="center">73.9</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.209)</td>
<td valign="top" align="center">43.0</td>
<td valign="top" align="center">179</td>
<td valign="top" align="center">45</td>
<td valign="top" align="center">223</td>
<td valign="top" align="center">18</td>
<td valign="top" align="center">186</td>
<td valign="top" align="center">2.08E-34</td>
<td valign="top" align="center">116</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B86">Yeoman et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.1)</td>
<td valign="top" align="center">40.9</td>
<td valign="top" align="center">105</td>
<td valign="top" align="center">126</td>
<td valign="top" align="center">229</td>
<td valign="top" align="center">56</td>
<td valign="top" align="center">158</td>
<td valign="top" align="center">4.11E-16</td>
<td valign="top" align="center">62.8</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.21)</td>
<td valign="top" align="center">46.0</td>
<td valign="top" align="center">76</td>
<td valign="top" align="center">159</td>
<td valign="top" align="center">234</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">74</td>
<td valign="top" align="center">5.59E-16</td>
<td valign="top" align="center">59.3</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.255)</td>
<td valign="top" align="center">33.3</td>
<td valign="top" align="center">120</td>
<td valign="top" align="center">107</td>
<td valign="top" align="center">220</td>
<td valign="top" align="center">17</td>
<td valign="top" align="center">126</td>
<td valign="top" align="center">2.93E-12</td>
<td valign="top" align="center">53.5</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.305)</td>
<td valign="top" align="center">45.4</td>
<td valign="top" align="center">99</td>
<td valign="top" align="center">96</td>
<td valign="top" align="center">194</td>
<td valign="top" align="center">176</td>
<td valign="top" align="center">267</td>
<td valign="top" align="center">4.81E-20</td>
<td valign="top" align="center">78.6</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.596)</td>
<td valign="top" align="center">34.3</td>
<td valign="top" align="center">233</td>
<td valign="top" align="center">69</td>
<td valign="top" align="center">266</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">248</td>
<td valign="top" align="center">2.33E-29</td>
<td valign="top" align="center">105</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS spaid-like (2132.146.peg.469)</td>
<td valign="top" align="center">33.7</td>
<td valign="top" align="center">237</td>
<td valign="top" align="center">66</td>
<td valign="top" align="center">300</td>
<td valign="top" align="center">12</td>
<td valign="top" align="center">219</td>
<td valign="top" align="center">7.15E-25</td>
<td valign="top" align="center">96.7</td>
<td valign="top" align="left"/></tr>
</tbody>
</table></table-wrap>
<table-wrap position="float" id="T4">
<label>TABLE 4</label>
<caption><p>Homology between ankyrin genes of two <italic>Spiroplasma ixodetis</italic> strains based on BLASTn search.</p></caption>
<table cellspacing="5" cellpadding="5" frame="hsides" rules="groups">
<thead>
<tr>
<td valign="top" align="left"><italic>Spiroplasma ixodetis</italic> gene (length)</td>
<td valign="top" align="center">Strain sHm ankyrin gene (length)</td>
<td valign="top" align="center">Identity</td>
<td valign="top" align="center">Aligned length</td>
<td valign="top" align="center" colspan="2"><italic>Spiroplasma ixodetis</italic> genes</td>
<td valign="top" align="center" colspan="2"><italic>s</italic>Hm genes</td>
<td valign="top" align="center"><italic>e</italic>-value</td>
<td valign="top" align="center">Bit score</td>
<td valign="top" align="left">References</td>
</tr>
<tr>
<td valign="top" align="center"></td>
<td valign="top" align="center"></td>
<td valign="top" align="center"></td>
<td valign="top" align="center"></td>
<td valign="top" align="center" colspan="2"><hr/></td>
<td valign="top" align="center" colspan="2"><hr/></td>
<td valign="top" align="center"></td>
<td valign="top" align="center"></td>
<td valign="top" align="center"></td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="center">Start (nt)</td>
<td valign="top" align="center">End (nt)</td>
<td valign="top" align="center">Start (nt)</td>
<td valign="top" align="center">End (nt)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/></tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">sCoc (JACSEQ010000039.1) (303 nt)</td>
<td valign="top" align="center">SHM_18920 (1,971 nt)</td>
<td valign="top" align="center">97</td>
<td valign="top" align="center">300</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">303</td>
<td valign="top" align="center">594</td>
<td valign="top" align="center">295</td>
<td valign="top" align="center">3.92E-144</td>
<td valign="top" align="center">505</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B76">Vera-Ponce Le&#x00F3;n et al., 2021</xref></td>
</tr>
<tr>
<td valign="top" align="left">sWSS (2132.146.peg.596) (894 nt)</td>
<td valign="top" align="center">SHM_18920 (1,971 nt)</td>
<td valign="top" align="center">97.6</td>
<td valign="top" align="center">894</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">894</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">894</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1535</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B86">Yeoman et al., 2019</xref></td>
</tr>
<tr>
<td valign="top" align="left">sWSS (2132.146.peg.469) (1656 nt)</td>
<td valign="top" align="center">SHM_21210 (1,370 nt)</td>
<td valign="top" align="center">96.2</td>
<td valign="top" align="center">974</td>
<td valign="top" align="center">114</td>
<td valign="top" align="center">1,087</td>
<td valign="top" align="center">414</td>
<td valign="top" align="center">1,380</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1,587</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS (2132.146.peg.209) (558 nt)</td>
<td valign="top" align="center">SHM_12270 (459 nt)</td>
<td valign="top" align="center">85.7</td>
<td valign="top" align="center">385</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">383</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">383</td>
<td valign="top" align="center">2.78E-113</td>
<td valign="top" align="center">403</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS (2132.146.peg.21) (276 nt)</td>
<td valign="top" align="center">SHM_12270 (459 nt)</td>
<td valign="top" align="center">96.8</td>
<td valign="top" align="center">158</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">158</td>
<td valign="top" align="center">265</td>
<td valign="top" align="center">422</td>
<td valign="top" align="center">6.55E-72</td>
<td valign="top" align="center">265</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS (2132.146.peg.255) (723 nt)</td>
<td valign="top" align="center">SHM_14030 (249 nt)</td>
<td valign="top" align="center">97.2</td>
<td valign="top" align="center">221</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">221</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">221</td>
<td valign="top" align="center">7.94E-105</td>
<td valign="top" align="center">375</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sWSS (2132.146.peg.305) (966 nt)</td>
<td valign="top" align="center">SHM_05900 (279 nt)</td>
<td valign="top" align="center">90.4</td>
<td valign="top" align="center">220</td>
<td valign="top" align="center">671</td>
<td valign="top" align="center">890</td>
<td valign="top" align="center">77</td>
<td valign="top" align="center">279</td>
<td valign="top" align="center">4.01E-74</td>
<td valign="top" align="center">274</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_03750) (162 nt)</td>
<td valign="top" align="center">SHM_00770 (177 nt)</td>
<td valign="top" align="center">97.5</td>
<td valign="top" align="center">162</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">162</td>
<td valign="top" align="center">16</td>
<td valign="top" align="center">177</td>
<td valign="top" align="center">1.33E-75</td>
<td valign="top" align="center">278</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B54">Martin et al., 2020</xref></td>
</tr>
<tr>
<td valign="top" align="left">sDa (SDA_06930) (438 nt)</td>
<td valign="top" align="center">SHM_05900 (279 nt)</td>
<td valign="top" align="center">87.9</td>
<td valign="top" align="center">241</td>
<td valign="top" align="center">269</td>
<td valign="top" align="center">506</td>
<td valign="top" align="center">56</td>
<td valign="top" align="center">279</td>
<td valign="top" align="center">4.73E-72</td>
<td valign="top" align="center">267</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_19590) (348 nt)</td>
<td valign="top" align="center">SHM_08510 (1,113 nt)</td>
<td valign="top" align="center">94.6</td>
<td valign="top" align="center">546</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">546</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">544</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">846</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_19580) (249 nt) &#x002A;NANK</td>
<td valign="top" align="center">SHM_08510 (1,113 nt)</td>
<td valign="top" align="center">95.9</td>
<td valign="top" align="center">249</td>
<td valign="top" align="center">249</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">637</td>
<td valign="top" align="center">884</td>
<td valign="top" align="center">1.46E-112</td>
<td valign="top" align="center">403</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_10430) (978 nt)</td>
<td valign="top" align="center">SHM_12110 (978 nt)</td>
<td valign="top" align="center">98.1</td>
<td valign="top" align="center">978</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">978</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">978</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1,707</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_08770) (723 nt)</td>
<td valign="top" align="center">SHM_12270 (459 nt)</td>
<td valign="top" align="center">94.1</td>
<td valign="top" align="center">292</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">292</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">290</td>
<td valign="top" align="center">3.45E-125</td>
<td valign="top" align="center">444</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_12020) (723 nt)</td>
<td valign="top" align="center">SHM_14030 (249 nt)</td>
<td valign="top" align="center">96.8</td>
<td valign="top" align="center">221</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">221</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">221</td>
<td valign="top" align="center">3.10E-103</td>
<td valign="top" align="center">370</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_05330) (591 nt)</td>
<td valign="top" align="center">SHM_18920 (1,971 nt)</td>
<td valign="top" align="center">87.7</td>
<td valign="top" align="center">236</td>
<td valign="top" align="center">50</td>
<td valign="top" align="center">285</td>
<td valign="top" align="center">1,082</td>
<td valign="top" align="center">1,314</td>
<td valign="top" align="center">7.66E-73</td>
<td valign="top" align="center">272</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_05340) (538 nt)</td>
<td valign="top" align="center">SHM_21210 (1,370 nt)</td>
<td valign="top" align="center">94.9</td>
<td valign="top" align="center">736</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">736</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">730</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1,149</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_01840) (876 nt)</td>
<td valign="top" align="center">SHM_28080 (693 nt)</td>
<td valign="top" align="center">89.8</td>
<td valign="top" align="center">690</td>
<td valign="top" align="center">49</td>
<td valign="top" align="center">735</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">690</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">883</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDa (SDA_01841) (231 nt)</td>
<td valign="top" align="center">SHM_28070 (162 nt)</td>
<td valign="top" align="center">93.8</td>
<td valign="top" align="center">162</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">162</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">161</td>
<td valign="top" align="center">4.40E-65</td>
<td valign="top" align="center">243</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDis (WP_252318998.1_58) (738 nt)</td>
<td valign="top" align="center">SHM_12270 (459 nt)</td>
<td valign="top" align="center">85.974</td>
<td valign="top" align="center">385</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">383</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">383</td>
<td valign="top" align="center">7.99E-115</td>
<td valign="top" align="center">409</td>
<td valign="top" align="left"><xref ref-type="bibr" rid="B63">Pollmann et al., 2022</xref></td>
</tr>
<tr>
<td valign="top" align="left">sDis (WP_252319959.1_15) (648 nt)</td>
<td valign="top" align="center">SHM_18920 (1,971 nt)</td>
<td valign="top" align="center">97.651</td>
<td valign="top" align="center">596</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">596</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">596</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1,024</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDis (WP_252320693.1_6) (975 nt)</td>
<td valign="top" align="center">SHM_08510 (1,113 nt)</td>
<td valign="top" align="center">87.514</td>
<td valign="top" align="center">913</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">904</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">910</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">1,044</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDis (WP_252321112.1_1) (483 nt)</td>
<td valign="top" align="center">SHM_21210 (1,370 nt)</td>
<td valign="top" align="center">96.312</td>
<td valign="top" align="center">461</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">461</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">461</td>
<td valign="top" align="center">0</td>
<td valign="top" align="center">758</td>
<td valign="top" align="left"/></tr>
<tr>
<td valign="top" align="left">sDis (WP_252319264.1_36, Epsilon-like toxin) (948 nt) &#x002A;NANK</td>
<td valign="top" align="center">SHM_25300 (495 nt) &#x002A;NAK</td>
<td valign="top" align="center">99.187</td>
<td valign="top" align="center">492</td>
<td valign="top" align="center">154</td>
<td valign="top" align="center">645</td>
<td valign="top" align="center">1</td>
<td valign="top" align="center">492</td>
<td valign="top" align="center">0.00E + 00</td>
<td valign="top" align="center">887</td>
<td valign="top" align="left"/></tr>
</tbody>
</table>
<table-wrap-foot>
<fn id="t4fns1"><p>&#x002A;NANK, non-ankyrin genes.</p></fn>
</table-wrap-foot>
</table-wrap>
<p>We then focused on genes conserved among <italic>Spiroplasma</italic> strains. Distantly related <italic>Spiroplasma</italic> species such as <italic>S. ixodetis</italic> (<italic>s</italic>Hm), <italic>S. poulsonii</italic> (<italic>s</italic>Mel), <italic>S. apis</italic> B31, <italic>S. citri</italic> BLH-MB, and <italic>S. syrphidicola</italic> EA-1 shared 345 protein clusters (<xref ref-type="fig" rid="F3">Figure 3A</xref>). For <italic>S. ixodetis</italic> strains, two MK strains (<italic>s</italic>Hm and <italic>s</italic>Da) and two non-MK strains (<italic>s</italic>Coc and <italic>s</italic>Dis) shared 595 protein clusters (<xref ref-type="fig" rid="F3">Figure 3A</xref>). In addition, MK strains <italic>s</italic>Hm and <italic>s</italic>Da possessed additional 219 conserved protein clusters. <italic>s</italic>Hm also harbored strain-specific 77 protein clusters (470 genes) associated with metabolism and transposition (<xref ref-type="fig" rid="F3">Figure 3B</xref> and <xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>) as well as many putative Type IV secretory system effector genes (<italic>n</italic> = 144, based on T4SEpre prediction at EffectiveDB, <xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>), some of which were located in the prophage regions. In <italic>Spiroplasma</italic>, RIP toxin irreversibly inactivates eukaryotic cytosolic ribosomes (<xref ref-type="bibr" rid="B31">Hamilton et al., 2016</xref>; <xref ref-type="bibr" rid="B12">Ballinger et al., 2019</xref>; <xref ref-type="bibr" rid="B27">Garcia-Arraez et al., 2019</xref>). Based on our blast searches, RIP-4 encoded by <italic>Spiroplasma</italic> endosymbiont of <italic>Drosophila neotestacea</italic> (ASM46790.1) showed low homology to SHM_22560 (79&#x2013;286 aa, <italic>e</italic>-value 6.7E-13, bit-score 60.8). Besides, SHM_22560 (hypothetical protein, 788 aa, <xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>) was predicted to contain a RIP domain based on Interpro (hit: IPR016138, aligned length: 111&#x2013;286 aa) and HHpred searches [hit: Sapolin (ID: 3HIQ), aligned length: 105&#x2013;344 aa, <italic>e</italic>-value: 2.3E-29]. A homolog of an epsilon-like toxin (WP_252319264.1_36) encoded by CI-inducing <italic>s</italic>Dis was detected in the <italic>s</italic>Hm genome (SHM_25300, <xref ref-type="table" rid="T4">Table 4</xref>), while AbiEii abortive infection toxin (WP_252320055.1_19) and OTU-like cysteine protease (WP_252320277.1_1) were not detected.</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption><p>Comparison of <italic>Spiroplasma</italic> genomes and ankyrin genes. <bold>(A&#x2013;B)</bold> Protein clusters conserved within <italic>Spiroplasma</italic> species (<italic>S. apis, S. citri, S. ixodetis, S. poulsonii</italic>, <italic>and S. syrphidicola</italic>) <bold>(A)</bold> and within <italic>S</italic>. <italic>ixodetis</italic> strains (<italic>s</italic>Hm, <italic>s</italic>Da, <italic>s</italic>Coc, and <italic>s</italic>Dis) <bold>(B)</bold>. Venn diagrams were visualized using OrthoVenn2. The <italic>s</italic>Hm-specific protein clusters and their functions are shown in <xref ref-type="supplementary-material" rid="TS1">Supplementary Table 1</xref>. MK, male-killing strain; NMK, non-male-killing strain; CI, cytoplasmic incompatibility strain. <bold>(C)</bold> Phylogeny of ankyrin genes in <italic>Spiroplasma</italic> strains <italic>s</italic>Hm and <italic>s</italic>Da. Numbers indicates nucleotide length (nt). Other domains of the genes are highlighted in different colors. Red: ankyrin; Blue: signal peptide; Green: OTU; Gray: transmembrane helix; Orange: cyclin-dependent kinase inhibitor; Purple: ubiquitination associated FEM1A_DROME; Sky blue: DNA J; Khaki: Ribosome&#x2013;inactivating protein (RIP); Black: molting protein (MLT-4).</p></caption>
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</fig>
<p>Although <italic>spaid</italic> gene is the only ankyrin-coding gene identified in the genome of strain <italic>s</italic>Mel (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>), <italic>s</italic>Hm carried 10 ankyrin genes (<xref ref-type="fig" rid="F3">Figure 3C</xref>). Some ankyrin genes harbored additional domains, such as those encoding for DnaJ (SHM_12110), cyclin-dependent kinase inhibitor (SHM_12110 and SHM_28080), and the protein ubiquitination associated FEM1A_DROME (SHM_21210); however, they did not encode for signal peptides, ovarian tumor-like deubiquitinase (OTU), or helix domains found in the <italic>spaid</italic> gene of strain <italic>s</italic>Me1 (<xref ref-type="bibr" rid="B59">Paredes et al., 2015</xref>; <xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>; <xref ref-type="bibr" rid="B56">Masson et al., 2018</xref>; <xref ref-type="bibr" rid="B28">Gerth et al., 2021</xref>). <italic>Wolbachia</italic> induces CI by the CI-inducing factors (Cif) harboring ankyrin repeats in insects (<xref ref-type="bibr" rid="B48">LePage et al., 2017</xref>). <xref ref-type="bibr" rid="B63">Pollmann et al. (2022)</xref> reported that CI-inducing <italic>s</italic>Dis strain did not harbor the <italic>cif</italic> gene. Similarly, <italic>s</italic>Hm-encoding 10 ankyrin genes has low homologies to those of other bacteria such as <italic>Wolbachia</italic> and <italic>Rickettsia</italic> and were not homologous to the <italic>cif</italic> as well as <italic>spaid</italic> genes. Intriguingly, MK <italic>s</italic>Da and CI <italic>s</italic>Dis strains had 11 and 12 ankyrin genes, respectively. These findings suggest that <italic>S. ixodetis</italic> has similar characteristics to <italic>Wolbachia</italic> endosymbionts (<xref ref-type="bibr" rid="B21">Duplouy et al., 2013</xref>; <xref ref-type="bibr" rid="B5">Arai et al., 2022b</xref>) in terms of phenotypes (i.e., CI and MK) and genetic compositions (i.e., multiple ankyrin genes). Some ankyrin genes encoded by <italic>S. poulsonii</italic> and <italic>Wolbachia</italic> have been implicated in reproductive manipulation (<xref ref-type="bibr" rid="B48">LePage et al., 2017</xref>; <xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>), and the ankyrin genes found in the <italic>s</italic>Hm genome may also be involved in MK mechanisms.</p>
</sec>
<sec id="S3.SS4">
<title>Male-killing genes of sHm are different from those of other male-killers in <italic>Homona magnanima</italic></title>
<p><italic>Homona magnanima</italic> harbors three different types of MK endosymbionts (i.e., <italic>Spiroplasma s</italic>Hm, Partiti-like virus OGVs, and <italic>Wolbachia w</italic>Hm-t strain), some of which can coinfect the same host (<xref ref-type="bibr" rid="B8">Arai et al., 2020</xref>; <xref ref-type="bibr" rid="B71">Takamatsu et al., 2021</xref>). Moreover, microbes sharing the same niche frequently exchange virulence-associated genes (<xref ref-type="bibr" rid="B44">Kent and Bordenstein, 2010</xref>; <xref ref-type="bibr" rid="B83">Wiedenbeck and Cohan, 2011</xref>). However, we found that strain <italic>s</italic>Hm did not harbor any gene homologous to those of MK Partiti-like virus OGVs (<xref ref-type="bibr" rid="B26">Fujita et al., 2021</xref>). Moreover, strain <italic>s</italic>Hm did not harbor <italic>wmk</italic> or effector genes (e.g., CifB-like) that are present on the MK-associated prophage WO<italic>w</italic>Hm-t76 region of strain <italic>w</italic>Hm-t (<xref ref-type="bibr" rid="B8">Arai et al., 2020</xref>, <xref ref-type="bibr" rid="B5">2022b</xref>). The <italic>wmk</italic> gene, a candidate gene for <italic>Wolbachia</italic>-induced MK (<xref ref-type="bibr" rid="B60">Perlmutter et al., 2019</xref>, <xref ref-type="bibr" rid="B61">2021</xref>; <xref ref-type="bibr" rid="B5">Arai et al., 2022b</xref>), possesses a helix-turn-helix (HTH) domain containing putative transcriptional regulator. Although no <italic>wmk</italic> homologs were identified, strain <italic>s</italic>Hm harbored 87 HTH domain-encoding genes, namely putative transposase (classified into IS-30, IS-3, and IS-5 type transposase, <italic>n</italic> = 83), a type II toxin-antitoxin system antitoxin <italic>HipB</italic> (SHM_ 03650), an AAA family ATPase (SHM_24830), an XRE family transcriptional regulator (SHM_17560), and a helix-turn-helix transcriptional regulator (SHM_05440). Notably, a putative transposase SHM_03660, encoded by a gene adjacent to <italic>s</italic>Hm-specific <italic>HipB</italic>-like SHM_3650, was homologous to the <italic>Wolbachia</italic> transcriptional regulator. Recently, <xref ref-type="bibr" rid="B6">Arai et al. (2022c)</xref> demonstrated that strains <italic>s</italic>Hm, <italic>w</italic>Hm-t, and OGVs affect <italic>H. magnanima</italic> males in different manners. Specifically, both strains <italic>s</italic>Hm and <italic>w</italic>Hm-t trigger abnormal apoptosis and interfere with sex determination in male embryos (manifested by the alteration of <italic>doublesex</italic> gene splicing), but only strain <italic>w</italic>Hm-t impairs the dosage-compensation system of the host (manifested by the alteration of the global gene expression on sex chromosomes). In contrast, the OGVs do not affect sex-determination cascades or dosage-compensation systems. These findings and our current results support the view that phylogenetically distinct microbes have independently developed different MK machinery even for the same host, i.e., <italic>H. magnanima</italic>. Therefore, an unknown factor in the <italic>s</italic>Hm genome may be responsible for the embryonic male death of <italic>H. magnanima</italic>.</p>
</sec>
<sec id="S3.SS5">
<title>sHm may require high infection density to kill <italic>Homona magnanima</italic> males</title>
<p>We observed that one of the sublines of the MK S+ line ceased to induce MK (<xref ref-type="fig" rid="F4">Figure 4A</xref>). This subline, referred to as the S+M+ line, exhibited stable <italic>s</italic>Hm infections for at least four generations. We simultaneously re-sequenced the genome of strain <italic>s</italic>Hm from S+M+ and S+ lines at the second-generation stage since their divergence. We previously demonstrated from a genomic comparison of MK <italic>Wolbachia</italic> (<italic>w</italic>Hm-t) and non-MK <italic>Wolbachia</italic> (<italic>w</italic>Hm-c) that an MK-associated 76 kb prophage region was inserted only in <italic>w</italic>Hm-t (<xref ref-type="bibr" rid="B5">Arai et al., 2022b</xref>). Similarly, we mapped the MK and non-MK <italic>s</italic>Hm re-sequenced Illumina reads to the complete <italic>s</italic>Hm genome (main chromosome and two plasmids) but did not detect any large-scale structural variation (insertions or deletions) as observed in <italic>w</italic>Hm-t (<xref ref-type="fig" rid="F4">Figure 4B</xref>). On the other hand, we found mutations specific to the non-MK <italic>s</italic>Hm mutant (i.e., frameshifts or insertion of stop codons) in 21 genes encoding hypothetical proteins (<italic>n</italic> = 4), tyrosine-tRNA ligase (<italic>n</italic> = 1), and transposase (<italic>n</italic> = 16) (<xref ref-type="supplementary-material" rid="TS2">Supplementary Table 2</xref>). The 21 genes were found on the main chromosome, not in plasmids. Moreover, the <italic>s</italic>Hm density in the S+M+ line was lower than that in the S+ line (Steel&#x2013;Dwass test, <italic>P</italic> &#x003C; 0.05, <xref ref-type="fig" rid="F4">Figure 4C</xref>).</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption><p>Comparison of <italic>Spiroplasma</italic> strain <italic>s</italic>Hm in MK and non-MK <italic>Homona magnanima</italic> lines. <bold>(A)</bold> <italic>Spiroplasma</italic>-positive 1:1 sex ratio line (S+M+ line) was maintained for over four generations (G1&#x2013;G4), parallelly with the all-female S+ line. <bold>(B)</bold> Structural variations of the genome of <italic>Spiroplasma</italic> strain <italic>s</italic>Hm in the MK (S+) and non-MK (S+M+) <italic>H. magnanima</italic> lines were visualized <italic>via</italic> Gview software. No obvious structural variations (i.e., the red colored loci), specific to MK <italic>s</italic>Hm strain in the S+ matriline, were identified. Chr: main chromosome (2.1 Mb); pSHM 1: sHm plasmid 1 (20 Kb); pSHM 2: sHm plasmid 2 (16 Kb). <bold>(C)</bold> Abundance of <italic>Spiroplasma</italic> (based on copy numbers of <italic>RpoB</italic>) in adult females (0-day post eclosion) of S+M+ line and S+ line. The horizontal bar within the box represents the median. The upper and lower hinges of the box indicate upper quartile and lower quartile, respectively. Sample sizes (numbers of examined individuals) are indicated in parentheses. Different letters indicate significant differences between groups (Steel&#x2013;Dwass test, <italic>P</italic> &#x003C; 0.05).</p></caption>
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</fig>
<p>Rapid genetic evolution leading to resistance against MK <italic>Spiroplasma</italic> has been reported in various hosts, such as the lacewing (<xref ref-type="bibr" rid="B33">Hayashi et al., 2018</xref>) and the planthopper (<xref ref-type="bibr" rid="B87">Yoshida et al., 2021</xref>). However, we can exclude the host genetic changes from the possible cause of the observed loss of MK phenotype because females of the S+ and S+M+ lines were parallelly mated with the males of the genetically homogeneous NSR line that had been maintained <italic>via</italic> inbreeding in the laboratory for over 10 years (&#x003E;120 generations).</p>
<p><italic>Spiroplasma</italic>-induced phenotypic changes have been repeatedly observed in previous studies. For example, spontaneous loss of MK was found in <italic>S. poulsonii</italic> strains of <italic>Drosophila</italic> flies, wherein substitutions and deletions occurred in the MK gene <italic>spaid</italic> (<xref ref-type="bibr" rid="B32">Harumoto and Lemaitre, 2018</xref>). Moreover, the MK strain <italic>S. poulsonii</italic> NSRO and its non-MK variant NSRO-A exhibit difference in bacterial densities in <italic>D. melanogaster</italic> (<xref ref-type="bibr" rid="B1">Anbutsu and Fukatsu, 2003</xref>). Indeed, bacterial density is one of the crucial factors for <italic>Spiroplasma</italic>- and <italic>Wolbachia</italic>-induced MK phenotype (<xref ref-type="bibr" rid="B38">Hurst and Jiggins, 2000</xref>; <xref ref-type="bibr" rid="B42">Kageyama et al., 2007</xref>; <xref ref-type="bibr" rid="B8">Arai et al., 2020</xref>). Based on these results, we speculate that the loss of MK phenotype of <italic>s</italic>Hm-infected <italic>H. magnanima</italic> was due to (i) reduced <italic>s</italic>Hm density and/or (ii) mutations in <italic>s</italic>Hm MK gene(s) or factors regulating MK gene expression levels. However, we still do not know how the small genomic rearrangements (i.e., inversions and insertions) detected in this study are involved in the phenotypic changes of <italic>s</italic>Hm. Future <italic>de novo</italic> genome construction of <italic>s</italic>Hm from S+M+ lines and gene function analysis would help in elucidating MK mechanisms.</p>
</sec>
<sec id="S3.SS6">
<title>Population dynamics and tissue tropism of sHm</title>
<p>Strain <italic>s</italic>Hm was abundant at the late-developmental stages of <italic>H. magnanima</italic> (<xref ref-type="fig" rid="F5">Figure 5A</xref>), and <italic>s</italic>Hm densities drastically increased from pupal to adult stages of the insect (<xref ref-type="fig" rid="F5">Figure 5B</xref>). In <italic>D. melanogaster</italic>, <italic>S. poulsonii</italic> copy numbers gradually increase as the host larval development proceeds and are generally higher in pupae than in larvae (<xref ref-type="bibr" rid="B1">Anbutsu and Fukatsu, 2003</xref>). In contrast to <italic>S. poulsonii</italic>, which is reported to be the most abundant in hemolymph (<xref ref-type="bibr" rid="B1">Anbutsu and Fukatsu, 2003</xref>, <xref ref-type="bibr" rid="B2">2006</xref>), strain <italic>s</italic>Hm exhibited low density in the hemolymph and high density in Malpighian tubules in the fifth instar larva stage (<xref ref-type="fig" rid="F5">Figure 5C</xref>). High titers in Malpighian tubules are also a characteristic of <italic>Wolbachia</italic>; <italic>Wolbachia</italic> present in Malpighian tubules protects the host from RNA-virus infections and may constitute a secondary pool of vertically infected bacteria (<xref ref-type="bibr" rid="B25">Faria and Sucena, 2013</xref>; <xref ref-type="bibr" rid="B62">Pietri et al., 2016</xref>). The localization of strain <italic>s</italic>Hm in somatic tissues may have contributed to the fitness of <italic>H. magnanima</italic> Although there have been no reports of <italic>S. ixodetis</italic> localization patterns in insects, our findings suggest that <italic>S. poulsonii</italic> and <italic>S. ixodetis</italic> have distinct proliferation strategies. The hemolymph is a nutrient-rich environment but is likely an extreme habitat for microorganisms because it is well-defended by the immune system of the host (<xref ref-type="bibr" rid="B15">Blow and Douglas, 2019</xref>). Indeed, only a few microbial taxa are known to persist in the hemolymph of insects for extended periods without causing insect morbidity and death (<xref ref-type="bibr" rid="B15">Blow and Douglas, 2019</xref>). Intriguingly, <italic>S. poulsonii s</italic>Mel encoded more metabolic genes in its genome than <italic>S. ixodetis s</italic>Hm (<xref ref-type="supplementary-material" rid="TS3">Supplementary Table 3</xref>). Hemolymph-inhabiting <italic>S. poulsonii</italic> may have developed specific adaptations for its habitat, which are distinct from those of <italic>S. ixodetis</italic>. Further characterization of genomic features and localization patterns of <italic>Spiroplasma</italic> strains will clarify the distinct proliferation strategies of the two species (e.g., nutrient requirements).</p>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption><p>Propagation and localization of strain <italic>s</italic>Hm in <italic>H. magnanima</italic>. <italic>Spiroplasma</italic> densities deduced from <italic>RpoB</italic> copy numbers per 10 ng DNA <bold>(A)</bold> and <italic>Spiroplasma</italic> densities deduced from <italic>RpoB</italic> copy numbers per individual <bold>(B)</bold> at each developmental stage. <bold>(C)</bold> Relative <italic>Spiroplasma</italic> density in each organ deduced from <italic>Spiroplasma RpoB</italic> copy numbers per host <italic>Ef1</italic>&#x03B1; copy. Hc, hemocyte; Fb, fat body; Mg, midgut; Mpg, Malpighian tubules; Tr, trachea; Hly, hemolymph. Different letters indicate significant differences between groups (Steel&#x2013;Dwass test, <italic>P</italic> &#x003C; 0.05).</p></caption>
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</fig>
</sec>
<sec id="S3.SS7">
<title>Proliferation of sHm in insect cell culture</title>
<p><xref ref-type="bibr" rid="B75">Tsugeno et al. (2017)</xref> reported that <italic>s</italic>Hm is horizontally transmitted by inoculating non-infected <italic>H. magnanima</italic> with concentrated hemolymph collected from <italic>s</italic>Hm-infected <italic>H. magnanima</italic>. Moreover, we revealed that <italic>S. ixodetis s</italic>Hm exhibited <italic>Wolbachia</italic>-like genetic characteristics (i.e., multiple ankyrin genes) and localization patterns in somatic tissues. <italic>Wolbachia</italic> can infect and be maintained stably in insect cell lines derived from insect taxa that are distantly related to their native hosts (<xref ref-type="bibr" rid="B24">Fallon, 2021</xref>). To examine whether <italic>s</italic>Hm can infect insect cells, we transinfected <italic>s</italic>Hm to the cell lines of <italic>A. albopictus</italic> (AeAl2) and <italic>B. mori</italic> (aff3), which are known to be susceptible to <italic>Wolbachia</italic>. <italic>s</italic>Hm proliferated successfully by placing a piece of fat bodies or Malpighian tubules derived from an S+ female larva into a flask containing the AeAl2 or aff3 cells (<xref ref-type="fig" rid="F6">Figure 6</xref>). <italic>s</italic>Hm was stably maintained in the cell lines for 12 weeks (<xref ref-type="fig" rid="F6">Figure 6A</xref>) but not in cell-free medium IPL-41. qPCR revealed that <italic>s</italic>Hm titers in AeAl2 cells were significantly higher at 12 weeks than at 4 weeks after the introduction of <italic>s</italic>Hm (<xref ref-type="fig" rid="F6">Figure 6B</xref>). This implies the potential of <italic>s</italic>Hm to survive in a wide host range besides <italic>Homona</italic> (<xref ref-type="bibr" rid="B75">Tsugeno et al., 2017</xref>), such as other lepidopteran and dipteran insects. <italic>S. ixodetis</italic> strains isolated from Japanese ticks were also shown to be culturable in the <italic>A. albopictus</italic> cell line C6/36 (<xref ref-type="bibr" rid="B73">Thu et al., 2019</xref>). We hypothesize that <italic>S. ixodetis</italic> strains have a broad host range like that of <italic>Wolbachia</italic>. It is not clear whether <italic>S. poulsonii</italic> has a broad host range because there is no but one report by <xref ref-type="bibr" rid="B29">Hackett et al. (1986)</xref> that showed the infectivity of strain WSRO (derived from <italic>D. willistoni</italic>) in the <italic>Trichoplusia ni</italic> cell line IPLB-TN-R<sup>2</sup>. Several attempts to transinfect <italic>S. poulsonii</italic> (strain NSRO; derived from <italic>D. nebulosa</italic>) and MK <italic>Spiroplasma</italic> (derived from the lacewing <italic>Mallada desjardinsi</italic>) into AeAl2 and aff3 cells failed (personal observation by DK). It has been shown by hemolymph injection that <italic>S. poulsonii</italic> can infect drosophilid flies but not houseflies, suggesting its narrow host range (<xref ref-type="bibr" rid="B84">Williamson and Poulson, 1979</xref>).</p>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption><p>Transinfection of <italic>Spiroplasma</italic> strain <italic>s</italic>Hm into mosquito and silkworm cell lines. <bold>(A)</bold> Detections of strain <italic>s</italic>Hm in passaged cells. Numbers indicate periods (weeks) from the transinfection. P (positive control): S + female; N (negative control): NSR female. <bold>(B)</bold> <italic>Spiroplasma</italic> density in AeAl2 cells deduced from <italic>RpoB</italic> copy numbers per 10 ng DNA. Different letters indicate significant differences between groups (Steel&#x2013;Dwass test, <italic>P</italic> &#x003C; 0.05).</p></caption>
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</fig>
</sec>
<sec id="S3.SS8">
<title>Summary and perspectives</title>
<p>In this study, we sequenced and analyzed the genome of an MK <italic>S. ixodetis</italic> strain <italic>s</italic>Hm. <italic>S. poulsonii</italic> possesses the Spaid toxin as the MK factor, whereas our study revealed that MK <italic>S. ixodetis</italic> did not harbor <italic>spaid</italic> homologs. We speculate that MK <italic>S. ixodetis</italic> strains found in a diverse range of insects (<xref ref-type="bibr" rid="B37">Hurst et al., 1999</xref>; <xref ref-type="bibr" rid="B40">Jiggins et al., 2000</xref>; <xref ref-type="bibr" rid="B67">Simon et al., 2011</xref>; <xref ref-type="bibr" rid="B69">Tabata et al., 2011</xref>; <xref ref-type="bibr" rid="B66">Sanada-Morimura et al., 2013</xref>) harbor yet-unknown MK gene(s), other than <italic>spaid</italic>; thus, future studies should focus on the identification of these MK genes. Besides, high infection efficiencies of strain <italic>s</italic>Hm in other insect cells led us to speculate that MK <italic>S. ixodetis</italic> has been horizontally transmitted among insect species, like <italic>Wolbachia</italic>, which has expanded its host range (<xref ref-type="bibr" rid="B88">Zhou et al., 1998</xref>; <xref ref-type="bibr" rid="B11">Baldo et al., 2006</xref>). Further studies would be required to understand whether closely related MK <italic>Spiroplasma</italic> strains (i.e., the <italic>S. ixodetis</italic> group) share common or different MK mechanisms, which will answer evolutionary questions such as how frequent novel MK genes arose, how MK genes moved between different <italic>Spiroplasma</italic> strains (if it did), and whether MK genes are associated with host sex determining systems.</p>
</sec>
</sec>
<sec id="S4" sec-type="data-availability">
<title>Data availability statement</title>
<p>All sequence data are available at DRA under BioProject: <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="PRJDB14468">PRJDB14468</ext-link>, Biosamples: <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SAMD00547685">SAMD00547685</ext-link>, <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="SAMD00547900">SAMD00547900</ext-link>, and <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="DRA014961">DRA014961</ext-link>. Spiroplasma genome data are available in the DDBJ database under the following accession numbers: <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="AP026933">AP026933</ext-link>&#x2013;<ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="AP026935">AP026935</ext-link>.</p>
</sec>
<sec id="S5">
<title>Author contributions</title>
<p>HA conducted all experiments, data analysis, and wrote the original manuscripts. MI assisted insect rearing, experiments, and discussions. DK managed the experiments and revised the original manuscript. All authors approved the final version of the manuscript.</p>
</sec>
</body>
<back>
<sec id="S6" sec-type="funding-information">
<title>Funding</title>
<p>This study was supported by the Japan Society for the Promotion of Science (JSPS) Research Fellowships for Young Scientists (grant numbers: 19J13123 and 21J00895), JSPS Grant-in-Aid for Scientific Research (grant number: 22K14902), and Cabinet Office, Government of Japan, Cross-ministerial Moonshot Agriculture, Forestry and Fisheries Research and Development Program (grant number: JPJ009237).</p>
</sec>
<ack><p>We thank Dr. Akiya Jouraku [National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, Japan] for providing <italic>H. magnanima</italic> genome data.</p>
</ack>
<sec id="S7" 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="S8" 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>
<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.2022.1075199/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fmicb.2022.1075199/full#supplementary-material</ext-link></p>
<supplementary-material xlink:href="Table_1.XLSX" id="TS1" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table_2.XLSX" id="TS2" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="Table_3.XLSX" id="TS3" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" xmlns:xlink="http://www.w3.org/1999/xlink"/>
</sec>
<glossary>
<title>Abbreviations</title>
<def-list id="DL1">
<def-item><term>CI</term><def><p>cytoplasmic incompatibility</p></def></def-item>
<def-item><term>FBS</term><def><p>fetal bovine serum</p></def></def-item>
<def-item><term>HTH</term><def><p>helix-turn-helix</p></def></def-item>
<def-item><term>JSPS</term><def><p>Japan Society for the Promotion of Science</p></def></def-item>
<def-item><term>MK</term><def><p>male-killing</p></def></def-item>
<def-item><term>OGV</term><def><p>Osugoroshivirus</p></def></def-item>
<def-item><term>OTU</term><def><p>operational taxonomic unit</p></def></def-item>
<def-item><term>RIP</term><def><p>ribosome-inactivating protein</p></def></def-item>
<def-item><term>WGA</term><def><p>whole genome amplification.</p></def></def-item>
</def-list>
</glossary>
<fn-group>
<fn id="footnote1">
<label>1</label>
<p><ext-link ext-link-type="uri" xlink:href="https://www.ebi.ac.uk/interpro/">https://www.ebi.ac.uk/interpro/</ext-link></p></fn>
<fn id="footnote2">
<label>2</label>
<p><ext-link ext-link-type="uri" xlink:href="https://orthovenn2.bioinfotoolkits.net/home">https://orthovenn2.bioinfotoolkits.net/home</ext-link></p></fn>
<fn id="footnote3">
<label>3</label>
<p><ext-link ext-link-type="uri" xlink:href="https://server.gview.ca">https://server.gview.ca</ext-link></p></fn>
<fn id="footnote4">
<label>4</label>
<p><ext-link ext-link-type="uri" xlink:href="https://www.bv-brc.org">https://www.bv-brc.org</ext-link></p></fn>
<fn id="footnote5">
<label>5</label>
<p><ext-link ext-link-type="uri" xlink:href="https://www.r-project.org/">https://www.r-project.org/</ext-link></p></fn>
</fn-group>
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