Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage
Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage
复制标题
纤毛虫的比较基因组学分析为“Nassophorea-Synhymenia-Phyllopharyngea”组合的进化历史提供了见解
DOI：
10.3389/fmicb.2019.02819
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发表时间：
2019-12-12
影响因子：
5.2
通讯作者：
Miao, Miao
中科院分区：
文献类型：
--
作者：
Pan, Bo;Chen, Xiao;Miao, Miao
纤毛虫原生动物（纤毛虫）被广泛用于研究进化，主要是由于它们在早期进化分支后成功辐射。本研究采用高通量测序技术，对纤毛虫系统学和进化研究中的一个难题--合膜虫属（Synhymenia）以及鼻咽纲（Nassophorea）和叶咽纲（Phyllopharyngea）的系统位置进行了研究。我们从一种合膜虫（Chilodontopsis depressa）和其他六种叶咽虫（Chilodochona sp.，Dysteria derouxi，Hartmannula sinica，Trithigmostoma cucullulus，Trochilia petrani和Trochilia sp.）。基于157个包含173，835个氨基酸残基的直向同源基因的系统基因组学分析揭示了C.在Phyllopharyngea纲内的扁囊藻，以及Nassophorea的单系性，这强烈支持Synhymenia作为Phyllopharyngea纲内的一个亚纲的分配。比较基因组分析进一步揭示了C.与Phyllopharyngea相比，C.扁叶藻与叶咽藻相似。功能富集分析表明，C.与Phyllopharyngea相似，而与Nassophorea相似。这些结果表明，基因组和转录组数据可以用来提供洞察内的进化关系的“Nassophorea-Synhymenia-Phyllopharyngea”组合。
Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.