The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the ‘Opisthosporidia hypothesis’). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the ‘Aphelida+Fungi hypothesis’). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (A. insulamus and A. tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida+Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favour of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia.

中文翻译：

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系统基因组学支持蚜虫和真菌的单系性并鉴定新的分子同源性

全菌门超群由真菌和单细胞生物的几个相关谱系（核菌门、罗泽菌门、微孢子虫和蚜虫门）组成，代表真核生物系统发育的主要分支之一。然而，除了核菌门作为第一个分化的全菌门分支的公认地位外，其他谱系之间的关系迄今为止仍未得到解决，这主要是由于缺乏某些类群的分子数据。值得注意的是，蚜虫是一类鲜为人知的内生吞噬原生生物，以具有纤维素壁的藻类为食。包括蚜虫在内的第一个分子系统发育支持了它们与 Rozellida 和 Microsporidia 的姐妹关系，它们共同形成了一个称为 Opisthosporidia 的新类群（“后孢子虫假说”）。然而，最近的系统发育分析，包括来自两个蚜虫属（Paraphelidium 和 Amoeboaphelidium）的大量序列数据，表明蚜虫是真菌的姐妹（“蚜虫+真菌假说”）。如果这一立场得到证实，单螺杆菌将成为了解全菌门早期进化和真菌起源的关键。在这里，我们在对两种蚜虫属（A. insulamus 和 A. tribonematis）的转录组进行测序后，对蚜虫进行了扩大分类学采样的系统发育分析，以测试这些相互竞争的假设。我们新的系统发育学分析（包括来自三个已知的蚜虫属的物种）强烈否定了后孢子虫假说。此外，比较基因组分析通过鉴定这两个谱系独有的 19 个直系同源基因，进一步支持了蚜虫+真菌假说。其中 7 个起源于蚜虫-真菌分裂之前的古代水平基因转移事件，其余 12 个可能从头进化，构成了该进化枝的额外分子同源性。基于我们已解决的全菌门系统发育学的祖先性状重建表明，真菌和罗泽尔科动物的祖先都是类蚜虫，具有变形鞭毛虫状态，并且可能以内生方式捕食含纤维素的细胞壁生物体。我们建议将其称为 Phytophagea 和 Opisthophagea 的两个谱系是从这个祖先进化而来的。噬菌体，分为蚜虫和经典真菌，主要专门从事藻类细胞的内生捕食。真菌在失去吞噬营养而有利于渗透营养后从这个谱系中出现。后噬菌门（Opisthophagea），包括罗泽尔科动物和微孢子虫，成为寄生虫，主要是含有几丁质的宿主。这个谱系进入了一个渐进的还原过程，导致了独特的生活方式，特别是在高度衍生的微孢子虫中。