Repository containing alignments of microsporidia genes related to the manuscript titled: "Variation in genome architecture and epigenetic modification across the microsporidia phylogeny"

AbstractMicrosporidia are a model clade for studying intracellular parasitism, being well-known for their streamlined genomes and their extreme life history. Although microsporidia are highly diverse and ecologically important to a broad range of hosts, previous research on genome architecture has focused primarily on the mammal-infecting genus <i>Encephalitozoon</i>. Here, we expand that work, testing the universality of the patterns observed in <i>Encephalitozoon</i> by investigating and comparing variation in genetic and epigenetic architectures in the high-quality genome assemblies of several major microsporidia clades. Our comparison of nine genomes, including the first genome assemblies of <i>Binucleata daphniae</i>, <i>Gurleya</i> <i>vavrai</i>, and <i>Conglomerata obtusa</i>, and revised, improved assemblies of <i>Glugoides intestinalis</i>, <i>Mitosporidium daphniae</i>,<i> </i>and <i>Ordospora colligata</i>, found limited conservation of genetic and epigenetic architecture across all microsporidia, although many genomic characteristics, such as nucleotide composition and repeat content, were shared between genomes of the same or related clades. For example, rRNA genes were hypermethylated in all species, but their position close to chromosome ends was only found in the <i>Encephalitozoon </i>and its sister clade. GC-content varied widely, linked to genome size, phylogenetic position and activity of repeat elements. These findings enhance our insight into genome evolution and, consistent with findings from other systems, suggest epigenetic modification as a regulatory mechanism of gene expression and repeat element activity in microsporidia. Our comparative genome analysis reveals high variation in genetic and epigenetic architecture among microsporidia, despite all of them adapting to a parasitic lifestyle within host cells.We identified single-copy orthologs among the species using proteinortho v.6.3.0 (Klemm et al., 2023), aligned the individual genes using MAFFT v.7.508 (Katoh et al., 2002; Katoh &amp; Standley, 2013), trimmed the alignments using trimAl v.1.4.rev15 (Capella-Gutiérrez et al., 2009) with the -automated1 flag, and concatenated them.

摘要：微孢子虫（Microsporidia）是研究胞内寄生现象的模式演化支，其以精简的基因组与极端的生活史特征而闻名。尽管微孢子虫类群多样性极高，且对广泛的宿主类群具有重要的生态学意义，但此前针对其基因组结构的研究主要集中于感染哺乳动物的脑孢虫属（Encephalitozoon）。本研究拓展了此前的研究范畴，通过对多个主要微孢子虫演化支的高质量基因组组装开展分析，比较其遗传与表观遗传结构的变异情况，以此检验脑孢虫属中观测到的基因组模式是否具有普遍性。本研究对9个基因组展开比较分析，其中包含达氏双核虫（Binucleata daphniae）、古尔莱虫（Gurleya vavrai）、钝顶团孢虫（Conglomerata obtusa）的首次基因组组装结果，以及肠道格氏虫（Glugoides intestinalis）、水蚤微孢虫（Mitosporidium daphniae）与聚团鄂尔多斯孢虫（Ordospora colligata）的修订优化组装版本。分析发现，尽管同演化支或近缘演化支的基因组在核苷酸组成、重复序列含量等诸多基因组特征上存在共通性，但所有微孢子虫的遗传与表观遗传结构保守性普遍较低。例如，所有物种的核糖体RNA（rRNA）基因均呈现高甲基化状态，但这类基因靠近染色体末端的分布特征仅见于脑孢虫属及其姊妹演化支。基因组GC含量差异显著，且与基因组大小、系统发育位置以及重复元件的活性密切相关。本研究结果加深了我们对微孢子虫基因组演化的认知，同时与其他研究系统的结论一致，表明表观遗传修饰是微孢子虫基因表达与重复元件活性的调控机制之一。尽管所有微孢子虫均演化出了宿主细胞内的寄生生活方式，但本比较基因组分析揭示了不同类群间遗传与表观遗传结构存在高度变异。本研究使用proteinortho v.6.3.0（Klemm等，2023）鉴定了物种间的单拷贝直系同源基因；使用MAFFT v.7.508（Katoh等，2002；Katoh与Standley，2013）对单个基因进行序列比对；使用trimAl v.1.4.rev15（Capella-Gutiérrez等，2009）并结合-automated1参数对比对结果进行修剪，最终将序列进行拼接。