IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish
Zhang, Shan1,2; Zhao, Jindong1,2,3; Yao, Meng1,2
Corresponding AuthorYao, Meng(yaom@pku.edu.cn)
2020-09-26
Source PublicationMETHODS IN ECOLOGY AND EVOLUTION
ISSN2041-210X
Pages17
AbstractAccurate 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.
Keywordbiomonitoring DNA metabarcoding environmental DNA fish barcode freshwater biodiversity in silico PCR primers
DOI10.1111/2041-210X.13485
Funding OrganizationSecond 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
Indexed BySCI ; SCI
Language英语
Funding ProjectSecond 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 Research AreaEnvironmental Sciences & Ecology
WOS SubjectEcology
WOS IDWOS:000572686100001
WOS KeywordENVIRONMENTAL DNA ; FRESH-WATER ; SPECIES IDENTIFICATION ; BIODIVERSITY ; COMMUNITIES ; MARINE ; DESIGN ; TOOL ; PCR
PublisherWILEY
Funding OrganizationSecond 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
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/38882
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorYao, Meng
Affiliation1.Peking Univ, Sch Life Sci, Beijing, Peoples R China
2.Peking Univ, Inst Ecol, Coll Urban & Environm Sci, Beijing, Peoples R China
3.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan, Peoples R China
Recommended Citation
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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