DNA barcoding of coastal ray-finned fishes in Vietnam

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.

基于细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I, COI）基因片段的DNA条形码（DNA barcoding）技术，已被广泛应用于物种鉴定与生物多样性研究。本研究旨在构建越南沿海辐鳍鱼类（ray-finned fishes）的综合条形码数据库。研究共从越南北部、中部和南部的鱼类上岸站点采集了3638份标本，成功获得765条辐鳍鱼类的COI序列，隶属于458个物种、273个属、113个科以及43个目。其中59个物种为越南新记录种，另有6个物种的序列为基因银行（GenBank）与生命条形码数据系统（BOLD）在线数据库的首次收录序列。仅32个物种无法被鉴定至物种水平，原因在于形态学鉴定存在难度，且这些物种与最相似序列的Kimura双参数（Kimura-2-Parameter, K2P）遗传距离均超过2%。此外，部分物种的种内遗传距离同样高于2%，暗示存在疑似隐存物种。各分类层级的平均K2P遗传距离分别为：种内0.34%、属内12.14%、科内17.39%、目内21.42%、纲内24.80%。越南北部、中部和南部海域的物种组成差异显著，三地仅存在16个共有物种。这一现象或与越南3260公里海岸线沿线多样的生境与环境因素相关。本研究结果证实，DNA条形码技术是越南沿海鱼类鉴定的高效可靠工具，同时构建了该类群鱼类的可靠DNA条形码参考文库。该DNA条形码数据将为未来越南渔业监测、保护与管理工作的优化提供重要支撑。