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题名: A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates
作者: Wang, Pu1; Gao, Feng1; Huang, Jie1, 3; Strueder-Kypke, Michaela4; Yi, Zhenzhen1, 2
刊名: ZOOLOGICA SCRIPTA
发表日期: 2015-09-01
DOI: 10.1111/zsc.12122
卷: 44, 期:5, 页:574-585
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
类目[WOS]: Evolutionary Biology ; Zoology
研究领域[WOS]: Evolutionary Biology ; Zoology
英文摘要: Phylogenetic studies of ciliates are mainly based on the primary structure information of the nuclear genes. Some regions of the small subunit ribosomal RNA (SSU-rRNA) gene have distinctive secondary structures, which have demonstrated value as phylogenetic/taxonomic characters. In the current work, we predict the secondary structures of four variable regions (V2, V4, V7 and V9) in the SSU-rRNA gene of 45 urostylids. Structure comparisons indicate that the V4 region is the most effective in revealing interspecific relationships, while the V9 region appears suitable at the family level or higher. The V2 region also offers some taxonomic information, but is too conserved to reflect phylogenetic relationships at the family or lower level, at least for urostylids. The V7 region is the least informative. We constructed several phylogenetic trees, based on the primary sequence alignment and based on an improved alignment according to the secondary structures. The results suggest that including secondary structure information in phylogenetic analyses provides additional insights into phylogenetic relationships. Using urostylid ciliates as an example, we show that secondary structure information results in a better understanding of their relationships, for example generic relationships within the family Pseudokeronopsidae.
关键词[WOS]: MARINE UROSTYLID CILIATE ; MULTIGENE-BASED ANALYSES ; N. SP CILIOPHORA ; MOLECULAR PHYLOGENY ; FAMILY PSEUDOKERONOPSIDAE ; SYSTEMATIC POSITION ; STRUCTURE ALIGNMENT ; SOUTHERN CHINA ; MIXED MODELS ; WEB SERVER
语种: 英语
WOS记录号: WOS:000359702400009
ISSN号: 0300-3256
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内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/25885
Appears in Collections:水生生物多样性与资源保护研究中心_期刊论文

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作者单位: 1.Ocean Univ China, Inst Evolut & Marine Biodivers, Lab Protozool, Qingdao 266003, Peoples R China
2.S China Normal Univ, Coll Life Sci, Lab Protozool, Key Lab Ecol & Environm Sci Guangdong Higher Educ, Guangzhou 510631, Guangdong, Peoples R China
3.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China
4.Univ Guelph, Dept Mol & Cellular Biol, Guelph, ON N1G 2W1, Canada
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