陈治, 蔡杏伟, 张清凤, 李高俊, 马春来, 申志新. 海南岛淡水鱼类环境DNA宏条形码参考数据库的初步构建及比较分析[J]. 南方水产科学, 2022, 18(3): 1-12. DOI: 10.12131/20210339
引用本文: 陈治, 蔡杏伟, 张清凤, 李高俊, 马春来, 申志新. 海南岛淡水鱼类环境DNA宏条形码参考数据库的初步构建及比较分析[J]. 南方水产科学, 2022, 18(3): 1-12. DOI: 10.12131/20210339
CHEN Zhi, CAI Xingwei, ZHANG Qingfeng, LI Gaojun, MA Chunlai, SHEN Zhixin. Preliminary construction and comparative analysis of environmental DNA metabarcoding reference database of freshwater fishes in Hainan Island[J]. South China Fisheries Science, 2022, 18(3): 1-12. DOI: 10.12131/20210339
Citation: CHEN Zhi, CAI Xingwei, ZHANG Qingfeng, LI Gaojun, MA Chunlai, SHEN Zhixin. Preliminary construction and comparative analysis of environmental DNA metabarcoding reference database of freshwater fishes in Hainan Island[J]. South China Fisheries Science, 2022, 18(3): 1-12. DOI: 10.12131/20210339

海南岛淡水鱼类环境DNA宏条形码参考数据库的初步构建及比较分析

Preliminary construction and comparative analysis of environmental DNA metabarcoding reference database of freshwater fishes in Hainan Island

  • 摘要: 为确定海南岛淡水鱼类环境DNA研究的最优参考数据库及最优目标基因,比较了自建数据库与公共数据库在COI、12S、16S 3个条形码片段上的物种覆盖度、注释准确率及种间差异阈值。结果表明:1) 实地采集鱼类72种,其中有16 (COI)、20 (12S) 和22 (16S) 种鱼类的参考序列为该研究首次提供;2) 仅有68.06% (COI)、66.67% (12S) 和69.44% (16S) 的鱼类在公共数据库比对到高相似度序列;3) 自建数据库对两个数据库共有鱼类的物种注释准确率显著高于公共数据库 (COI: 100% vs 69.64%; 12S: 96.15% vs 67.30%; 16S: 96% vs 70%);4) COI基因是判别海南岛淡水鱼类的最优目标基因,16S次之;5) 基于K2P遗传距离确定的种间差异阈值分别为0.006 9 (COI)、0.005 6 (12S) 和0.007 5 (16S),其物种判别准确率为94.96% (COI)、89.05% (12S)和92.70% (16S)。结果表明自建数据库优于公共数据库,建议使用COI、16S作为海南岛淡水鱼类环境DNA宏条形码基因。

     

    Abstract: In order to determine the optimal reference database and target genes for environmental DNA study of freshwater fishes in Hainan Island, we compared the species coverage, annotation accuracy and threshold values of interspecific difference of COI, 12S and 16S between the self-built database and the public database. The results show that: 1) Seventy-two fish species were collected, among which 16 (COI), 20 (12S) and 22 (16S) species' reference sequences were provided for the first time. 2) Only 68.06% (COI), 66.67% (12S) and 69.44% (16S) of the fish had high similarity sequence in the public database. 3) The annotation accuracy based on the self-built database was significantly higher than that on the public database (COI: 100% vs 69.64%; 12S: 96.15% vs 67.30%; 16S: 96% vs 70%). 4) COI gene was the best target gene for identifying freshwater fishes in Hainan Island, followed by 16S gene. 5) The threshold values of interspecific difference based on K2P genetic distance were 0.006 9 (COI), 0.005 6 (12S) and 0.007 5 (16S), respectively, and the accuracy rates were 94.96% (COI), 89.05% (12S) and 92.70% (16S), respectively. This study reveals that the sequence annotation accuracy of the self-built database is significantly higher than that of the public database, and it is suggested that COI and 16S should be used as the environmental DNA metabarcoding genes of freshwater fishes in Hainan Island.

     

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