Methodology for fish biodiversity monitoring with environmental DNA metabarcoding:The primers,databases and bioinformatic pipelines  

作　　者：Fan Xiong Lu Shu Honghui Zeng Xiaoni Gan Shunping He Zuogang Peng 

机构地区：[1]State Key Laboratory of Freshwater Ecology and Biotechnology,Institute of Hydrobiology,Chinese Academy of Sciences,Wuhan,430072,China [2]Key Laboratory of Freshwater Fish Reproduction and Development(Ministry of Education),Southwest University School of Life Sciences,Chongqing,400715,China

出　　处：《Water Biology and Security》2022年第1期63-72,共10页水生生物与安全（英文）

基　　金：supported by the grant from the Graduate Student Research Innovation Project of Chongqing(CYB20093)。

摘　　要：Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodiversity monitoring.Several reviews concerning fish eDNA have focused on standard sampling methods and its applications,though a systematic review focused on marker genes,databases,and bioinformatic pipelines has not yet been published.Here,we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring.We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA,and then discuss reference barcoding databases,relevant bioinformatic analyses,as well as developed pipelines.The performances of universal primers and their relevant reference databases are summarized.Combined use of multiple primer pairs targeted for more than one gene marker(e.g.,12S,16S,Cytb,COI),and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses.We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool.Ultimately,we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.

关 键 词：Environmental DNA Fish biodiversity Metabarcoding METHODOLOGY 

分 类 号：Q149[生物学—生态学]