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A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish

文献类型：期刊论文

作者Zhang, Shan1,3; Zhao, Jindong1,2,3; Yao, Meng1,3
刊名METHODS IN ECOLOGY AND EVOLUTION
出版日期2020-09-26
页码17
关键词biomonitoring DNA metabarcoding environmental DNA fish barcode freshwater biodiversity in silico PCR primers
ISSN号2041-210X
DOI10.1111/2041-210X.13485
通讯作者Yao, Meng(yaom@pku.edu.cn)
英文摘要Accurate assessments of fish species diversity and community composition are essential for understanding fish ecology and conservation management. Environmental DNA (eDNA) metabarcoding has become an integrated method for monitoring fish species. The accuracy and efficacy of eDNA metabarcoding rely heavily on the choice of primers used for PCR amplification. A wide selection of metabarcoding primers for fish has been developed; however, there exists no comprehensive and comparative evaluation of their amplification or taxonomic classification of a rich diversity of fish species, which hinders informed decisions regarding their suitability for different study systems. Here we reviewed the literature and compiled a list of 22 primer sets for eDNA-based metabarcoding analysis of teleost fish, the performance of which was compared using in silico PCR, followed by in vitro metabarcoding analysis using eDNA from waterbodies in Beijing, which harbour a high number of freshwater fish species. We found that the primers showed considerable differences in the amplified taxonomic ranges and proportions, fish taxa richness, species discrimination power and fish community compositions, both in silico and in vitro. The number of fish taxa detected from eDNA by the primer sets varied from 0 to 66. Primers targeting the 12S rRNA gene generally detected greater fish diversity than those targeting the 16S rRNA or COI genes, while primers targeting the cytochromebgene amplified the fewest fish taxa in vitro. Regarding target genes, 12S primers generally outperformed other primers in terms of amplified fish diversity. The results of in silico PCR and in vitro tests were not always in agreement, suggesting that primer choice for biodiversity surveys should not be based solely on in silico evaluation. The use of different primers can qualitatively and quantitatively affect the detected biodiversity and these effects should be considered in experimental design and data interpretation. These results will assist with primer selection for eDNA-based fish surveys, and consequently support conservation of freshwater biodiversity.
WOS关键词ENVIRONMENTAL DNA ; FRESH-WATER ; SPECIES IDENTIFICATION ; BIODIVERSITY ; COMMUNITIES ; MARINE ; DESIGN ; TOOL ; PCR
资助项目Second Tibetan Plateau Scientific Expedition and Research Program (STEP)[2019QZKK0304] ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP)[2019QZKK0503] ; State Key Laboratory of Freshwater Ecology and Biotechnology[2020FB10] ; National Science and Technology Basic Resources Survey Program of China[2019FY101700]
WOS研究方向Environmental Sciences & Ecology
语种英语
WOS记录号WOS:000572686100001
出版者WILEY
资助机构Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; Second Tibetan Plateau Scientific Expedition and Research Program (STEP) ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; State Key Laboratory of Freshwater Ecology and Biotechnology ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China ; National Science and Technology Basic Resources Survey Program of China
源URL[http://ir.ihb.ac.cn/handle/342005/38881]  
专题水生生物研究所_水生生物分子与细胞生物学研究中心_期刊论文
通讯作者Yao, Meng
作者单位1.Peking Univ, Sch Life Sci, Beijing, Peoples R China
2.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan, Peoples R China
3.Peking Univ, Inst Ecol, Coll Urban & Environm Sci, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Zhang, Shan,Zhao, Jindong,Yao, Meng. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish[J]. METHODS IN ECOLOGY AND EVOLUTION,2020:17.
APA Zhang, Shan,Zhao, Jindong,&Yao, Meng.(2020).A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish.METHODS IN ECOLOGY AND EVOLUTION,17.
MLA Zhang, Shan,et al."A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish".METHODS IN ECOLOGY AND EVOLUTION (2020):17.

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来源：水生生物研究所

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