title: Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea.
abstract: Scuticociliates and hymenostomes are two groups of the ciliate class Oligohymenophorea, a diverse clade that includes two model genera, Tetrahymena and Paramecium, which have been intensively studied due to their ease of culture and their amenability to a wide range of biochemical and genetic investigations. However, phylogenetic relationships among the subclasses of the Oligohymenophorea, and especially between the Scuticociliatia and Hymenostomatia, are not clearly resolved. Here, we investigate the phylogenetic relationship between the subclasses Scuticociliatia and Hymenostomatia based on omics data. The transcriptomes of five species, comprising four oligohymenophoreans and one colpodean, were sequenced. A supermatrix was constructed for phylogenomic analyses based on 113 genes encoding 43,528 amino acid residues from 26 taxa, including ten representatives of the class Oligohymenophorea. Our phylogenomic analyses revealed that the monophyletic Scuticociliatia is sister to the monophyletic Hymenostomatia, which together form the terminal branch within the monophyletic class Oligohymenophorea. Competing hypotheses for this relationship were rejected by topological tests. Our results provide corroborative evidence for the close relationship between the subclasses Scuticociliatia and Hymenostomatia, justifying the possible use of the model hymenostome T. thermophila as an effective experimental system to study the molecular and cellular biology of the scuticociliates.
authors.affiliation: Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China; Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: jennyfeng168@163.com.
authors.forename: Jin-Mei
authors.initials: JM
authors.lastname: Feng
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: jiangchuanqi7@163.com.
authors.forename: Chuan-Qi
authors.initials: CQ
authors.lastname: Jiang
authors.affiliation: Department of Life Sciences, Natural History Museum, London SW7 5BD, UK. Electronic address: a.warren@nhm.ac.uk.
authors.forename: Alan
authors.initials: A
authors.lastname: Warren
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: tianmiao0304@126.com.
authors.forename: Miao
authors.initials: M
authors.lastname: Tian
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China. Electronic address: CJ15972224484@163.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: liumang12712@gmail.com.
authors.forename: Guang-Long
authors.initials: GL
authors.lastname: Liu
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: xiongjie@ihb.ac.cn.
authors.forename: Jie
authors.initials: J
authors.lastname: Xiong
authors.affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: miaowei@ihb.ac.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Miao
mesh_terms: D001483:Base Sequence; D016798:Ciliophora / Q000235:genetics; D016802:Oligohymenophorea / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D012313:RNA / Q000032:analysis / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: Hymenostomatia; Oligohymenophorea; Phylogenomics analysis; Scuticociliatia