Data from: Phylogenomic diversity of archigregarine apicomplexans

<b>Abstract</b><br/><p>Gregarines are a large and diverse subgroup of Apicomplexa, a lineage of obligate animal symbionts including pathogens like <em>Plasmodium</em>, the malaria parasite. Unlike <em>Plasmodium</em>, however, gregarines are poorly studied, despite the fact that as early-branching apicomplexans they are crucial to our understanding of the origin and evolution of all apicomplexans and their parasitic lifestyle. Exemplifying this, the earliest branch of gregarines, the archigregarines, are particularly poorly studied: around 80 species have been described from marine invertebrates, but almost all of them were assigned to a single genus, <em>Selenidium</em>. Most are known only from light micrographs and largely unresolved rDNA phylogenies, where they exhibit a great deal of sequence variation, but fall into at least five subclades. To resolve the relationships within archigregarines, we sequenced 12 single-cell transcriptomes from species representing all four known subclades, as well as one blastogregarine (which frequently branch with <em>Selenidium</em>). A 190-gene phylogenomic tree confirmed fourmaximally-supported individual clades of archigregarines and blastogregarines. These clades are discrete and distantly related, and also correlate with host identity. We propose the establishment of three novel genera of archigregarines to reflect their phylogenetic diversity and host range, and nine novel species isolated from a range of marine invertebrates.</p>

摘要
簇虫（gregarines）是顶复门（Apicomplexa）下一个庞大且多样的类群，顶复门是一类专性动物共生生物谱系，包含疟原虫（Plasmodium，引发疟疾的病原体）等致病菌。然而与疟原虫不同，簇虫的研究程度较低；尽管作为早期分化的顶复门生物，它们对于我们理解所有顶复门生物的起源、演化以及其寄生生活方式至关重要。这一点在簇虫中最早分化的分支——原簇虫亚目（archigregarines）上体现得尤为明显：目前已从海洋无脊椎动物中描述了约80个物种，但其中几乎所有都被归入单一的塞勒啶虫属（Selenidium）。多数原簇虫仅通过光学显微镜图像被记录，且基于核糖体DNA（rDNA）的系统发育分析大多未能解决其分类关系：尽管它们存在大量序列变异，但至少可划分为5个亚支。为解析原簇虫亚目的内部亲缘关系，本研究对代表所有4个已知亚支的物种以及1个胚簇虫（blastogregarine，该类群常与塞勒啶虫属聚为一支）的12个单细胞转录组（transcriptomes）进行了测序。基于190个基因的系统发育组学树证实，原簇虫亚目与胚簇虫可分为4个得到最大支持度的独立演化支。这些演化支彼此独立且亲缘关系较远，同时与宿主种类存在相关性。为反映原簇虫亚目的系统发育多样性与宿主范围，本研究提议建立3个原簇虫亚目新属，并描述9个分离自多种海洋无脊椎动物的新物种。