Sun Zongyi, Jiang Chuanqi, Feng Jinmei, Yang Wentao, Li Ming, Miao Wei
Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, PR China.
Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan 430072, Hubei Province, PR China.
Parasite. 2017;24:43. doi: 10.1051/parasite/2017043. Epub 2017 Nov 14.
In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits and 119,141 transcripts. Then we obtained a final transcriptome, including 17.7 megabits and 35,560 transcripts, by removing contaminative and redundant sequences. Phylogenomic analysis based on a supermatrix with 132 genes comprising 53,873 amino acid residues and phylogenetic analysis based on SSU rDNA of 27 species were carried out herein to reveal the evolutionary relationships among six ciliate groups: Colpodea, Oligohymenophorea, Litostomatea, Spirotrichea, Heterotrichea and Protocruziida. The topologies of both phylogenomic and phylogenetic trees are discussed in this paper. In addition, our results suggest that single-cell sequencing is a sound method of obtaining sufficient omics data for phylogenomic analysis, which is a good choice for uncultivable ciliates. The transcriptome data for Balantidium ctenopharyngodoni are the first omics data within the subclass Trichostomatia, and provide a good basis for ciliate phylogenomic analysis, as well as related omics analysis.
在本文中，我们展示了1955年陈启鎏等从草鱼（Ctenopharyngodon idella）后肠中采集的栉毛虫（Balantidium ctenopharyngodoni）的转录组数据。我们评估了序列质量，并从头组装了一个初步转录组，其中包含43.3兆比特和119,141条转录本。然后，通过去除污染性和冗余序列，我们获得了一个最终转录组，其中包含17.7兆比特和35,560条转录本。本文基于一个由132个基因组成、包含53,873个氨基酸残基的超级矩阵进行了系统基因组分析，并基于27个物种的小亚基核糖体DNA（SSU rDNA）进行了系统发育分析，以揭示六个纤毛虫类群之间的进化关系：杯形纲（Colpodea）、寡膜纲（Oligohymenophorea）、唇口纲（Litostomatea）、旋毛纲（Spirotrichea）、异毛纲（Heterotrichea）和原克鲁兹亚纲（Protocruziida）。本文讨论了系统基因组树和系统发育树的拓扑结构。此外，我们的结果表明，单细胞测序是为系统基因组分析获取足够组学数据的可靠方法，这对于不可培养的纤毛虫来说是一个不错的选择。栉毛虫的转录组数据是口毛亚纲内的首个组学数据，为纤毛虫系统基因组分析以及相关组学分析提供了良好的基础。
