Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory of Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
Mol Phylogenet Evol. 2018 Dec;129:338-345. doi: 10.1016/j.ympev.2018.06.025. Epub 2018 Jun 15.
Ciliates are one of the eukaryotic unicellular organisms which are thought to be the oldest life forms, and widely geographically distributed. For a variety of reasons, some groups of ciliates have attracted more attention than others, such as the class Spirotrichea and related species with its complicated evolutionary relationships. In this study, we obtained the transcriptome data of three typical ciliates, Uroleptopsis citrina, Euplotes vannus, Protocruzia tuzeti using high throughput sequencing. The genetic relationships were revealed by phylogenomic analysis of 109 genes comprising of 34,882 amino acid residues, and analyses based on SSU rDNA of 55 species, as well as the comparison of gene content among spirotricheans and related species. Our phylogenomic analyses show the Spirotrichea is monophyletic when Protocruzia is excluded, in which four subclasses: Oligotrichia, Choreotrichia, Hypotrichia and Euplotia also formed momophyletic groups respectively. The Hypotrichia was placed as a sister branch to the assemblage, in which two oligotrichs clustered with two choreotrichs. In addition to this, the Protocruziidia was placed in an independent lineage status out of the Spirotrichea. Together with its high binding-related gene content compared to other species and the significant variation in morphological characters, these findings support the removal of Protocruzia from the class Spirotrichea.
纤毛虫是真核单细胞生物之一，被认为是最古老的生命形式，广泛分布于全球各地。由于各种原因，一些纤毛虫群体比其他群体受到了更多的关注，例如旋口类和与其进化关系复杂的相关物种。在这项研究中，我们使用高通量测序获得了三种典型纤毛虫（Uroleptopsis citrina、Euplotes vannus 和 Protocruzia tuzeti）的转录组数据。通过对包含 34882 个氨基酸残基的 109 个基因的系统基因组分析，以及基于 55 个物种的 SSU rDNA 分析，以及对旋口类和相关物种的基因含量进行比较，揭示了它们的遗传关系。我们的系统基因组分析表明，当排除 Protocruzia 时，旋口类是单系的，其中四个亚目：寡毛类、 choreotrichia、hypotrichia 和 euplotia 分别形成单系群。Hypotrichia 作为一个分支与集合体并列，其中两个寡毛类与两个 choreotrichs 聚类。除此之外，protocruziidia 被置于旋口类之外的独立谱系状态。与其他物种相比，它具有较高的结合相关基因含量和形态特征的显著变化，这些发现支持将 Protocruzia 从旋口类中移除。
