基于 RNA-Seq 数据的 Cladobranchia（腹足纲：裸鳃目）内的关系：初步研究。
Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation.
机构信息
Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology , University of Maryland, College Park , MD 20742, USA ; NMFS, National Systematics Laboratory , National Museum of Natural History, Smithsonian Institution , MRC-153, PO Box 37012, Washington, DC 20013, USA.
Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology , University of Maryland, College Park , MD 20742, USA.
出版信息
R Soc Open Sci. 2015 Sep 23;2(9):150196. doi: 10.1098/rsos.150196. eCollection 2015 Sep.
Cladobranchia (Gastropoda: Nudibranchia) is a diverse (approx. 1000 species) but understudied group of sea slug molluscs. In order to fully comprehend the diversity of nudibranchs and the evolution of character traits within Cladobranchia, a solid understanding of evolutionary relationships is necessary. To date, only two direct attempts have been made to understand the evolutionary relationships within Cladobranchia, neither of which resulted in well-supported phylogenetic hypotheses. In addition to these studies, several others have addressed some of the relationships within this clade while investigating the evolutionary history of more inclusive groups (Nudibranchia and Euthyneura). However, all of the resulting phylogenetic hypotheses contain conflicting topologies within Cladobranchia. In this study, we address some of these long-standing issues regarding the evolutionary history of Cladobranchia using RNA-Seq data (transcriptomes). We sequenced 16 transcriptomes and combined these with four transcriptomes from the NCBI Sequence Read Archive. Transcript assembly using Trinity and orthology determination using HaMStR yielded 839 orthologous groups for analysis. These data provide a well-supported and almost fully resolved phylogenetic hypothesis for Cladobranchia. Our results support the monophyly of Cladobranchia and the sub-clade Aeolidida, but reject the monophyly of Dendronotida.
被囊动物（腹足纲：裸鳃亚目）是一个多样化的（约 1000 种）但研究不足的海蛞蝓软体动物群。为了充分了解裸鳃亚目的多样性和 cladobranchia 内部特征的演化，需要对进化关系有一个坚实的理解。迄今为止，仅进行了两次直接尝试来理解 cladobranchia 内部的进化关系，但都没有产生支持良好的系统发育假设。除了这些研究，还有一些研究在调查更广泛的类群（裸鳃亚目和后鳃亚纲）的进化历史时，解决了这个类群内的一些关系。然而，所有产生的系统发育假说都包含 cladobranchia 内部相互矛盾的拓扑结构。在这项研究中，我们使用 RNA-Seq 数据（转录组）来解决 cladobranchia 进化历史中的一些长期存在的问题。我们测序了 16 个转录组，并将这些数据与来自 NCBI Sequence Read Archive 的 4 个转录组进行了组合。使用 Trinity 进行转录组装和使用 HaMStR 进行同源性确定，产生了 839 个用于分析的直系同源群。这些数据为 cladobranchia 提供了一个支持良好且几乎完全解决的系统发育假说。我们的结果支持 cladobranchia 和 aeolidida 亚群的单系性，但拒绝 dendronotida 的单系性。
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