The preliminary DNA barcoding dataset of fishes from Chinese coastal waters

Abstract

DNA barcoding is a molecular method for species identification based on a short standardized DNA sequence derived from the 5’ region of the cytochrome c oxidase subunit I (COI) gene, which is widely applied in marine fish identification. In this study, DNA barcodes were generated for 1,671 specimens representing 309 morphological marine fish species belonging to 223 genera and covering 101 families from Chinese coastal waters. The mean Kimura 2-parameter (K2P) genetic distances within species, genera, families, and orders were 0.20%, 20.94%, 24.45%, and 25.34%, respectively. As expected, the mean interspecific distance was higher than the mean intraspecific distance. Phylogenetic trees based on Bayesian inference (BI) and neighbor-joining (NJ) methods agreed with the taxonomic classifications. A total of 306 operational taxonomic units (OTUs) were reidentified via automatic barcode gap discovery (ABGD) analysis. An estimated nucleotide substitution matrices showed a transversion bias compared to transitional mutation. The amino acid variations of the barcoding region were also examined, and 13 amino acid sites exhibited high variability. Overall, our findings confirmed that DNA barcoding is a highly reliable mean of identifying fish species in Chinese coastal waters, and that the barcode library established here would facilitate the monitoring and management of the marine fishery resources in China.