| Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora) | |
Zhan, Zifeng1,2,3; Li, Ju1,3 ; Xu, Kuidong1,2,3,4
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| 2019-11-01 | |
| 发表期刊 | MICROORGANISMS
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| 卷号 | 7期号:11页码:25 |
| 通讯作者 | Xu, Kuidong(kxu@qdio.ac.cn) |
| 摘要 | Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence. |
| 关键词 | metabarcode DNA barcoding cryptic species secondary structure ITS1-5.8S-ITS2 mitochondrial COI rDNA |
| DOI | 10.3390/microorganisms7110493 |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助项目 | National Natural Science Foundation of China[41876171] ; National Natural Science Foundation of China[41476144] ; National Natural Science Foundation of China[41406171] ; National Natural Science Foundation of China[41876171] ; National Natural Science Foundation of China[41476144] ; National Natural Science Foundation of China[41406171] |
| WOS研究方向 | Microbiology |
| WOS类目 | Microbiology |
| WOS记录号 | WOS:000502273600016 |
| 出版者 | MDPI |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/163880 |
| 专题 | 海洋生物分类与系统演化实验室 |
| 通讯作者 | Xu, Kuidong |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao 266071, Shandong, Peoples R China 2.Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Biol & Biotechnol, Qingdao 266071, Shandong, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Shandong, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 第一作者单位 | 中国科学院海洋研究所; 中国科学院海洋大科学研究中心 |
| 通讯作者单位 | 中国科学院海洋研究所; 中国科学院海洋大科学研究中心 |
| 推荐引用方式 GB/T 7714 | Zhan, Zifeng,Li, Ju,Xu, Kuidong. Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)[J]. MICROORGANISMS,2019,7(11):25. |
| APA | Zhan, Zifeng,Li, Ju,&Xu, Kuidong.(2019).Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora).MICROORGANISMS,7(11),25. |
| MLA | Zhan, Zifeng,et al."Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)".MICROORGANISMS 7.11(2019):25. |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Ciliate Environmenta（5488KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
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