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
发表期刊LIMNOLOGY AND OCEANOGRAPHY-METHODS
ISSN1541-5856
页码11
通讯作者Xu, Kuidong(kxu@qdio.ac.cn)
摘要Diversity 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
收录类别SCI
语种英语
WOS研究方向Marine & Freshwater Biology ; Oceanography
WOS类目Limnology ; Oceanography
WOS记录号WOS:000482639600001
出版者WILEY
引用统计
被引频次:18[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.qdio.ac.cn/handle/337002/162871
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, 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
第一作者单位中国科学院海洋研究所
通讯作者单位中国科学院海洋研究所
推荐引用方式
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.
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
lom3.10330.pdf(1085KB)期刊论文出版稿限制开放CC BY-NC-SA浏览
Effects of intrageno(1034KB)期刊论文出版稿限制开放CC BY-NC-SA浏览
个性服务
推荐该条目
保存到收藏夹
查看访问统计
导出为Endnote文件
谷歌学术
谷歌学术中相似的文章
[Zhao, Feng]的文章
[Filker, Sabine]的文章
[Xu, Kuidong]的文章
百度学术
百度学术中相似的文章
[Zhao, Feng]的文章
[Filker, Sabine]的文章
[Xu, Kuidong]的文章
必应学术
必应学术中相似的文章
[Zhao, Feng]的文章
[Filker, Sabine]的文章
[Xu, Kuidong]的文章
相关权益政策
暂无数据
收藏/分享
文件名: lom3.10330.pdf
格式: Adobe PDF
文件名: 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.pdf
格式: Adobe PDF
所有评论 (0)
暂无评论
 

除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。