背景:圣孢子虫(Endomyxa,Rhizaria)是一组感染水生无脊椎动物的单细胞寄生虫。它们在海洋环境中越来越被认为是广泛和重要的,造成无脊椎动物水产养殖每年大量损失。尽管它们很重要,孢子虫的分子数据很少,迄今为止只发表了两个基因组集合体。因此,这些寄生虫的进化起源尚不清楚,包括它们的系统发育位置和伴随着从自由生活方式到寄生生活方式的转变的基因组适应。这里,我们测序并组装了三个新的天疱疮基因组,以及密切相关的两栖物种的基因组,为了研究系统发育,origin,和基因组适应寄生在圣孢子虫。
结果:使用系统学方法,我们证实了圣孢子虫的单系,并显示了带有Mikrocytida的副粘菌群,Haplosporida是这两组的姐妹。我们报告说,这些寄生虫的基因组相对较小(12-36Mb)和基因稀疏(〜2300-5200基因),同时含有令人惊讶的大量非编码序列(约70-90%的基因组)。执行基因家族的基因树感知祖先重建,我们证明了在隐孢子虫寄生起源的广泛基因丢失,主要是代谢功能,除了末端分支,几乎没有基因增加。最后,我们强调了一些在群体进化过程中经历了扩展的功能基因类别。
结论:我们从一个神秘但重要的无脊椎动物寄生虫谱系中提供了重要的新基因组信息,并阐明了一些基因组创新,伴随着该谱系向寄生虫的进化过渡。我们的结果和数据为制定针对这些寄生虫的控制措施提供了遗传基础。
BACKGROUND: Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea.
RESULTS: Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group.
CONCLUSIONS: We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.