| Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda | |
| Wu, Shu1,2; Xiong, Jie1; Yu, Yuhe1; Yu, YH (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China. | |
| 2015-06-24 | |
| Source Publication | PLOS ONE
 |
| ISSN | 1932-6203 |
| Volume | 10Issue:6Pages:e0131498 |
| Abstract | Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intraspecies (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy. |
| Subtype | Article |
| Department | [Wu, Shu ; Xiong, Jie ; Yu, Yuhe] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China ; [Wu, Shu] Univ Chinese Acad Sci, Beijing, Peoples R China |
| DOI | 10.1371/journal.pone.0131498 |
| WOS Headings | Science & Technology |
| Indexed By | SCI |
| Language | 英语 |
| WOS Research Area | Science & Technology - Other Topics |
| WOS Subject | Multidisciplinary Sciences |
| WOS ID | WOS:000356932500164 |
| WOS Keyword | INTERNAL TRANSCRIBED SPACER ; MITOCHONDRIAL-DNA SEQUENCES ; SPECIES DELIMITATION ; PHYLOGENETIC-RELATIONSHIPS ; CRUSTACEA COPEPODA ; MOLECULAR-DATA ; BIODIVERSITY ASSESSMENT ; EUKARYOTIC DIVERSITY ; BAYESIAN-INFERENCE ; RDNA |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ihb.ac.cn/handle/342005/23847 |
| Collection | 淡水生态学研究中心_期刊论文 |
| Corresponding Author | Yu, YH (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China. |
| Affiliation | 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China |
| Recommended Citation GB/T 7714 | Wu, Shu,Xiong, Jie,Yu, Yuhe,et al. Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda[J]. PLOS ONE,2015,10(6):e0131498. |
| APA | Wu, Shu,Xiong, Jie,Yu, Yuhe,&Yu, YH .(2015).Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda.PLOS ONE,10(6),e0131498. |
| MLA | Wu, Shu,et al."Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda".PLOS ONE 10.6(2015):e0131498. |
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| Taxonomic Resolution（1027KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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