Department of Food Science, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
Gene. 2012 Jan 1;491(1):40-8. doi: 10.1016/j.gene.2011.09.009. Epub 2011 Sep 21.
The development of DNA-based methods for the identification of fish species is important for fisheries research and control, as well as for the detection of unintentional or fraudulent species substitutions in the marketplace. The aim of this study was to generate a comprehensive reference database of DNA sequences from the mitochondrial 16S and 12S ribosomal RNA (rRNA) genes for 53 commercial fish species in South Africa and to evaluate the applicability of these genetic markers for the identification of fish at the species level. The DNA extracted from all target species was readily amplified using universal primers targeting both rRNA gene regions. Sequences from the 16S and 12S rRNA genes were submitted to GenBank for the first time for 34% and 53% of the fish species, respectively. Cumulative analysis of the 16S rRNA gene sequences revealed mean conspecific, congeneric and confamilial Kimura two parameter (K2P) distances of 0.03%, 0.70% and 5.10% and the corresponding values at the 12S level were 0.03%, 1.00% and 5.57%. K2P neighbour-joining trees based on both sequence datasets generally clustered species in accordance with their taxonomic classifications. The nucleotide variation in both the 16S and 12S sequences was suitable for identifying the large majority of the examined fish specimens to at least the level of genus, but was found to be less useful for the explicit differentiation of certain congeneric fish species. It is recommended that one or more faster-evolving DNA regions be analysed to confirm the identities of closely-related fish species in South Africa.
基于 DNA 的鱼类物种鉴定方法的发展对于渔业研究和控制以及市场上无意或欺诈性的物种替代检测都非常重要。本研究旨在为南非的 53 种商业鱼类生成线粒体 16S 和 12S 核糖体 RNA(rRNA)基因的 DNA 序列综合参考数据库，并评估这些遗传标记在物种水平上鉴定鱼类的适用性。使用针对两个 rRNA 基因区域的通用引物，从所有目标物种中提取的 DNA 都很容易扩增。16S 和 12S rRNA 基因的序列首次提交给 GenBank，分别占鱼类物种的 34%和 53%。16S rRNA 基因序列的累积分析显示，同种、同属和同科的 Kimura 两参数（K2P）距离分别为 0.03%、0.70%和 5.10%，相应的 12S 水平值分别为 0.03%、1.00%和 5.57%。基于两个数据集的 K2P 邻接树通常根据其分类学分类将物种聚类。16S 和 12S 序列中的核苷酸变异足以将大多数检查的鱼类标本识别到至少属的水平，但发现对于某些同属鱼类物种的明确区分不太有用。建议分析一个或多个进化较快的 DNA 区域，以确认南非亲缘关系密切的鱼类物种的身份。
