Chen Xiao, Zhao Xiaolu, Liu Xiaohui, Warren Alan, Zhao Fangqing, Miao Miao
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China.
Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China.
Protein Cell. 2015 May;6(5):373-385. doi: 10.1007/s13238-015-0147-3. Epub 2015 Apr 2.
Ciliates are one of the oldest living eukaryotic unicellular organisms, widely distributed in the waters around the world. As a typical marine oligotrich ciliate, Strombidium sulcatum plays an important role in marine food webs and energy flow. Here we report the first deep sequencing and analyses of RNA-Seq data from Strombidium sulcatum. We generated 42,640 unigenes with an N50 of 1,451 bp after de novo assembly and removing rRNA, mitochondrial and bacteria contaminants. We employed SPOCS to detect orthologs from S. sulcatum and 17 other ciliates, and then carried out the phylogenomic reconstruction using 127 single copy orthologs. In phylogenomic analyses, concatenated trees have similar topological structures with concordance tree on the class level. Together with phylogenetic networks analysis, it aroused more doubts about the placement of Protocruzia, Mesodinium and Myrionecta. While epiplasmic proteins are known to be related to morphological characteristics, we found the potential relationship between gene expression of epiplasmic proteins and morphological characteristics. This work supports the use of high throughput approaches for phylogenomic analysis as well as correlation analysis between expression level of target genes and morphological characteristics.
纤毛虫是现存最古老的真核单细胞生物之一，广泛分布于世界各地的水域中。作为一种典型的海洋寡毛类纤毛虫，沟痕急游虫在海洋食物网和能量流动中发挥着重要作用。在此，我们报告了首次对沟痕急游虫RNA测序数据进行的深度测序和分析。在进行从头组装并去除rRNA、线粒体和细菌污染物后，我们生成了42,640个单基因，其N50为1,451 bp。我们使用SPOCS从沟痕急游虫和其他17种纤毛虫中检测直系同源物，然后使用127个单拷贝直系同源物进行系统发育基因组重建。在系统发育基因组分析中，串联树在纲水平上具有与一致性树相似的拓扑结构。结合系统发育网络分析，这引发了对原克鲁虫属、中缢虫属和拟铃虫属分类位置的更多质疑。虽然已知表质蛋白与形态特征有关，但我们发现了表质蛋白基因表达与形态特征之间的潜在关系。这项工作支持使用高通量方法进行系统发育基因组分析以及目标基因表达水平与形态特征之间的相关性分析。
