title: Phylogenomics of non-model ciliates based on transcriptomic analyses.
abstract: 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.
authors.affiliation: 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.
authors.forename: Xiao
authors.initials: X
authors.lastname: Chen
authors.affiliation: Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China.
authors.forename: Xiaolu
authors.initials: X
authors.lastname: Zhao
authors.affiliation: College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK.
authors.forename: Alan
authors.initials: A
authors.lastname: Warren
authors.affiliation: Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China.
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
authors.affiliation: College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Miao
authors.initials: M
authors.lastname: Miao
mesh_terms: D016798:Ciliophora / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D016053:RNA, Protozoan / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000502:physiology*
chemical_list: D016053:RNA, Protozoan
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