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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
2019-11-01
Source PublicationMICROORGANISMS
Volume7Issue:11Pages:25
Corresponding AuthorXu, Kuidong(kxu@qdio.ac.cn)
AbstractMetabarcoding 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.
Keywordmetabarcode DNA barcoding cryptic species secondary structure ITS1-5.8S-ITS2 mitochondrial COI rDNA
DOI10.3390/microorganisms7110493
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[41876171] ; National Natural Science Foundation of China[41476144] ; National Natural Science Foundation of China[41406171]
WOS Research AreaMicrobiology
WOS SubjectMicrobiology
WOS IDWOS:000502273600016
PublisherMDPI
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/163880
Collection海洋生物分类与系统演化实验室
Corresponding AuthorXu, Kuidong
Affiliation1.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
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
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.
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