| 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
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| 2019-08-26 | |
| Source Publication | LIMNOLOGY AND OCEANOGRAPHY-METHODS
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| ISSN | 1541-5856 |
| Pages | 11 |
| Corresponding Author | Xu, Kuidong(kxu@qdio.ac.cn) |
| Abstract | 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. |
| DOI | 10.1002/lom3.10330 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Research Area | Marine & Freshwater Biology ; Oceanography |
| WOS Subject | Limnology ; Oceanography |
| WOS ID | WOS:000482639600001 |
| Publisher | WILEY |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.qdio.ac.cn/handle/337002/162871 |
| Collection | 海洋生物分类与系统演化实验室 |
| Corresponding Author | Xu, Kuidong |
| Affiliation | 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 |
| First Author Affilication | Institute of Oceanology, Chinese Academy of Sciences |
| Corresponding Author Affilication | Institute 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. |
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