IOCAS-IR  > 海洋生物分类与系统演化实验室
Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single-cell high-throughput DNA sequencing
Zhao, Feng1,2,3; Filker, Sabine4; Xu, Kuidong1,2,3,5; Li, Ju1; Zhou, Tong1,5; Huang, Pingping1,5
2019-08-26
Source PublicationLIMNOLOGY AND OCEANOGRAPHY-METHODS
ISSN1541-5856
Pages11
Corresponding AuthorXu, Kuidong(kxu@qdio.ac.cn)
AbstractDiversity assessments using the small subunit (SSU) rRNA gene allow for rapid assessments of microeukaryotic communities. Yet, for microeukaryotes, only limited information is available on the extent to which sequence variations within individual genomes exist at this locus. We investigated 14 marine species belonging to four major ciliate groups by single-cell high-throughput DNA sequencing to estimate the extent of intragenomic polymorphism in the V4 region of the SSU rRNA gene. Based on these results, we evaluated the potential effect of polymorphism on metabarcoding studies. The intragenomic variability was generally below 3% among about 1000 unique sequences obtained from each studied cell, except of Protocruzia sp., whose intragenomic variability was as high as 15.6% among about 2000 unique sequences. Intragenomic variations significantly correlated with the number of macronuclei, but not with the biovolume of cell or macronuclei, indicating the occurrence of nonuniform evolution within the macronuclei. The removal of rare unique sequences greatly decreased the number of variations. For diversity studies, we therefore propose to conservatively discard rare amplicons. Considering the intragenomic variation within the V4 region, a sequence similarity cutoff of 3% to delimit marine ciliate operational taxonomic units could be substantiated, as at least this threshold could exclude most effect of intragenomic polymorphisms, although it may be too strict for some particular groups.
DOI10.1002/lom3.10330
Indexed BySCI
Language英语
WOS Research AreaMarine & Freshwater Biology ; Oceanography
WOS SubjectLimnology ; Oceanography
WOS IDWOS:000482639600001
PublisherWILEY
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/162871
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, Shandong, Peoples R China
2.Pilot Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Shandong, Peoples R China
3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Shandong, Peoples R China
4.Univ Technol Kaiserslautern, Dept Mol Ecol, Kaiserslautern, Germany
5.Univ Chinese Acad Sci, Beijing, 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
Zhao, Feng,Filker, Sabine,Xu, Kuidong,et al. Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single-cell high-throughput DNA sequencing[J]. LIMNOLOGY AND OCEANOGRAPHY-METHODS,2019:11.
APA Zhao, Feng,Filker, Sabine,Xu, Kuidong,Li, Ju,Zhou, Tong,&Huang, Pingping.(2019).Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single-cell high-throughput DNA sequencing.LIMNOLOGY AND OCEANOGRAPHY-METHODS,11.
MLA Zhao, Feng,et al."Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single-cell high-throughput DNA sequencing".LIMNOLOGY AND OCEANOGRAPHY-METHODS (2019):11.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Zhao, Feng]'s Articles
[Filker, Sabine]'s Articles
[Xu, Kuidong]'s Articles
Baidu academic
Similar articles in Baidu academic
[Zhao, Feng]'s Articles
[Filker, Sabine]'s Articles
[Xu, Kuidong]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Zhao, Feng]'s Articles
[Filker, Sabine]'s Articles
[Xu, Kuidong]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.