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Abstract：
Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium-M. rubrum, M. major, and M. chamaeleon-being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination-particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate-requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
摘要：
最近的高通量测序努力已经产生了多基因/蛋白质系统发育，可以自信地解决纤毛门内的几种类间和类内关系。我们利用海洋微生物真核生物转录组测序项目的大规模测序工作，其他SRA提交，和可用的基因组数据，以及我们自己的测序工作，以确定Mesodinium的系统发育位置，并生成迄今为止分类最丰富的系统基因组纤毛虫树。不管数据挖掘策略如何，多蛋白数据集，或者进化的分子模型，我们一直在纤毛虫类之间恢复同样良好的关系，确认先前确定的许多更高级别的关系。Mesodinium总是与Litostomatea成员形成一个单系群，Mesodinium-M的兼养物种rubrum,M.少校，和M.chamaeleon-比异养成员更密切相关，M.pulex.Mesodinium作为其他litostomes姐妹的良好支持的位置与以前的分子分析形成鲜明对比，包括利用相同转录组数据库的系统基因组研究。这些拓扑差异说明了在挖掘混合物种转录组时需要谨慎，并表明在猎物污染中识别纤毛虫序列-特别是对于Mesodinium物种，其中被盗猎物核的表达似乎占主导地位-需要对包含序列的系统发育进行彻底和迭代的筛选来自大型猎物。
