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A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates
Wang, Pu1; Gao, Feng1; Huang, Jie1,3; Strueder-Kypke, Michaela4; Yi, Zhenzhen1,2
2015-09-01
Source PublicationZOOLOGICA SCRIPTA
ISSN0300-3256
Volume44Issue:5Pages:574-585
AbstractPhylogenetic 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.
SubtypeArticle
DOI10.1111/zsc.12122
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaEvolutionary Biology ; Zoology
WOS SubjectEvolutionary Biology ; Zoology
WOS KeywordMARINE UROSTYLID CILIATE ; MULTIGENE-BASED ANALYSES ; N. SP CILIOPHORA ; MOLECULAR PHYLOGENY ; FAMILY PSEUDOKERONOPSIDAE ; SYSTEMATIC POSITION ; STRUCTURE ALIGNMENT ; SOUTHERN CHINA ; MIXED MODELS ; WEB SERVER
WOS IDWOS:000359702400009
Citation statistics
Cited Times:11[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/25885
Collection水生生物多样性与资源保护研究中心
Affiliation1.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
Recommended Citation
GB/T 7714
Wang, Pu,Gao, Feng,Huang, Jie,et al. A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates[J]. ZOOLOGICA SCRIPTA,2015,44(5):574-585.
APA Wang, Pu,Gao, Feng,Huang, Jie,Strueder-Kypke, Michaela,&Yi, Zhenzhen.(2015).A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates.ZOOLOGICA SCRIPTA,44(5),574-585.
MLA Wang, Pu,et al."A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates".ZOOLOGICA SCRIPTA 44.5(2015):574-585.
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