Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl
Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl
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大规模系统发育分析为Oligohymenophorea（Protista，Ciliophora）的系统发育提供了新的见解，并建立了一个新的Urocentria亚纲。
DOI：
10.1016/j.ympev.2021.107112
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发表时间：
2021
影响因子：
4.1
通讯作者：
Gao Feng 唯一通讯
中科院分区：
文献类型：
--
作者：
Wang Chundi;Gao Yunyi;Lu Borong;Chi Yong;Zhang Tengteng;El-Serehy Hamed A.;Al-Farraj Saleh A.;Li Lifang;Song Weibo;Gao Feng 唯一通讯
寡囊纤毛虫纲是纤毛虫原生生物中最具多样性的类群之一，在基础生物学研究中具有重要意义，包括了解各类群之间的进化关系。该纲内的系统发育关系在很大程度上仍然难以捉摸，尤其是在Peniculia亚纲内，该亚纲包含长期存在问题的分类群尾丝藻和副鼻藻。在本研究中，我们测序的基因组和/或转录组的六个非可培养oligohyphorean使用单细胞测序技术。基于85个分类群的扩展分类群取样进行系统基因组学分析，包括编码36，953个氨基酸的157个核基因。结果表明：（1）尾中心虫形成一个独立的分支，与Scuticociliatia和Hymenostomatia形成的分支是姐妹分支，结合形态学资料，支持建立一个新的亚纲，尾中心虫属。亚类，在Oligohydrophorea内;（2）通过基因组分析和同源基因比较，揭示了拟囊虫属与Peniculines的亲缘关系，为将拟囊虫属从囊虫纲中删除，并将其提升为Peniculia亚纲中的拟囊虫目提供了佐证;（3）基于染色体组学分析和形态学数据，我们推测，Peritrichia是Oligohydrophorea中最早的分支，而Scuticociliatia和Hymenostomatia最常见祖先，其次是Urocentria和Peniculia。此外，终止密码子分析表明，寡聚体广泛使用UGA作为终止密码子，而UAR被重新分配给谷氨酸（peritrichs）或谷氨酰胺（其他），支持进化假说。
The class Oligohymenophorea is one of the most diverse assemblage of ciliated protists, which are particularly important in fundamental biological studies including understanding the evolutionary relationships among the lineages. Phylogenetic relationships within the class remain largely elusive, especially within the subclass Peniculia, which contains the long-standing problematic taxaUrocentrumandParanassula. In the present study, we sequenced the genomes and/or transcriptomes of six non-culturable oligohymenophoreans using single-cell sequencing techniques. Phylogenomic analysis was performed based on expanded taxon sampling of 85 taxa, including 157 nuclear genes encoding 36,953 amino acids. The results indicate that: (1) urocentrids form an independent branch that is sister to the clade formed by Scuticociliatia and Hymenostomatia, which, together with the morphological data, supports the establishment of a new subclass, Urocentria n. subcl., within Oligohymenophorea; (2) phylogenomic analysis and ortholog comparison reveal a close relationship betweenParanassulaand peniculines, providing corroborative evidence for removingParanassulafrom Nassulida and elevating it as an order, Paranassulida, within the subclass Peniculia; (3) based on the phylogenomic analyses and morphological data, we hypothesize that Peritrichia is the earliest diverging clade within Oligohymenophorea while Scuticociliatia and Hymenostomatia share the most common ancestor, followed successively by Urocentria and Peniculia. In addition, stop codon analyses indicate that oligohymenophoreans widely use UGA as the stop codon, while UAR are reassigned to glutamate (peritrichs) or glutamine (others), supporting the evolutionary hypothesis.