Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage

doi:10.3389/fmicb.2019.02819

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	Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage
	Pan, B ; Chen, X ; Hou, LN ; Zhang, QQ ; Qu, ZS ; Warren, A ; Miao, M
刊名	FRONTIERS IN MICROBIOLOGY
	2019-12-12
卷号	10 页码:2819
关键词	ciliated protozoa evolution introns phylogenetic relationship stop codon usage
ISSN号	1664-302X
DOI	10.3389/fmicb.2019.02819
产权排序	[Pan, Bo ; Qu, Zhishuai] Ocean Univ China, Inst Evolut & Marine Biodivers, Qingdao, Shandong, Peoples R China ; [Pan, Bo] Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Shandong, Peoples R China ; [Chen, Xiao] Columbia Univ, Med Ctr, Dept Genet & Dev, New York, NY USA ; [Hou, Lina ; Miao, Miao] Univ Chinese Acad Sci, Savaid Med Sch, Beijing, Peoples R China ; [Zhang, Qianqian] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai, Peoples R China ; [Qu, Zhishuai] Tech Univ Kaiserslautem, Ecol Grp, Kaiserslautern, Germany ; [Warren, Alan] Nat Hist Museum, Dept Life Sci, London, England
文献子类	Article
英文摘要	Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.
WOS关键词	CYTOPHARYNGEAL BASKET ; MACRONUCLEAR GENOME ; FINE-STRUCTURE ; CILIOPHORA ; PHYLOGENY ; SEQUENCE ; ULTRASTRUCTURE ; PROTEIN ; RECONSTRUCTION ; MORPHOLOGY
WOS研究方向	Microbiology
语种	英语
WOS记录号	WOS:000504720500001
资助机构	Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) [2018SDKJ0406-2] ; Natural Science Foundation of ChinaNational Natural Science Foundation of China [31672279, 31672251] ; Natural Science Foundation of Shandong ProvinceNatural Science Foundation of Shandong Province [JQ201706] ; University of Chinese Academy of SciencesChinese Academy of Sciences [Y8540XX1W2] ; China Scholarship CouncilChina Scholarship Council
内容类型	期刊论文
源URL	[http://ir.yic.ac.cn/handle/133337/24791]
专题	海岸带生物资源高效利用研究与发展中心烟台海岸带研究所_海岸带生物学与生物资源利用所重点实验室
作者单位	1.Ocean Univ China, Inst Evolut & Marine Biodivers, Qingdao, Shandong, Peoples R China; 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Shandong, Peoples R China; 3.Columbia Univ, Med Ctr, Dept Genet & Dev, New York, NY USA; 4.Univ Chinese Acad Sci, Savaid Med Sch, Beijing, Peoples R China; 5.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai, Peoples R China; 6.Tech Univ Kaiserslautem, Ecol Grp, Kaiserslautern, Germany; 7.Nat Hist Museum, Dept Life Sci, London, England
推荐引用方式 GB/T 7714	Pan, B,Chen, X,Hou, LN,et al. Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage[J]. FRONTIERS IN MICROBIOLOGY,2019,10:2819.
APA	Pan, B.,Chen, X.,Hou, LN.,Zhang, QQ.,Qu, ZS.,...&Miao, M.(2019).Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage.FRONTIERS IN MICROBIOLOGY,10,2819.
MLA	Pan, B,et al."Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage".FRONTIERS IN MICROBIOLOGY 10(2019):2819.