College of Marine Science, University of South Florida, Saint Petersburg, Florida, United States.
PeerJ. 2023 Mar 13;11:e15016. doi: 10.7717/peerj.15016. eCollection 2023.
A critical factor in fisheries management is the protection of spawning sites for ecologically and economically important fish species. DNA barcoding (., amplification and sequencing of the mitochondrial cytochrome c oxidase I (COI) gene) of fish eggs has emerged as a powerful technique for identifying spawning sites. However, DNA barcoding of individual fish eggs is time-consuming and expensive. In an attempt to reduce costs and effort for long-term fisheries monitoring programs, here we used DNA metabarcoding, in which DNA is extracted and amplified from a composited sample containing all the fish eggs collected at a given site, to identify fish eggs from 49 stations on the West Florida Shelf. A total of 37 taxa were recovered from 4,719 fish eggs. Egg distributions on the West Florida Shelf corresponded with the known habitat types occupied by these taxa, which included burrower, coastal pelagic, epipelagic, mesopelagic, demersal, deep demersal, commensal, and reef-associated taxa. Metabarcoding of fish eggs was faster and far less expensive than barcoding individual eggs; however, this method cannot provide absolute taxon proportions due to variable copy numbers of mitochondrial DNA in different taxa, different numbers of cells within eggs depending on developmental stage, and PCR amplification biases. In addition, some samples yielded sequences from more taxa than the number of eggs present, demonstrating the presence of contaminating DNA and requiring the application of a threshold proportion of sequences required for counting a taxon as present. Finally, we review the advantages and disadvantages of using metabarcoding . individual fish egg barcoding for long-term monitoring programs.
渔业管理的一个关键因素是保护生态和经济上重要的鱼类产卵场。鱼类卵的 DNA 条码技术（即线粒体细胞色素 c 氧化酶 I（COI）基因的扩增和测序）已成为识别产卵场的有力技术。然而，对单个鱼卵进行 DNA 条码技术分析既耗时又昂贵。为了降低长期渔业监测计划的成本和工作量，我们在这里使用了 DNA 代谢条码技术，该技术从在特定地点收集的所有鱼卵的组合样本中提取和扩增 DNA，以识别西佛罗里达架上 49 个站点的鱼卵。从 4719 个鱼卵中总共回收了 37 个分类单元。西佛罗里达架上的卵分布与这些分类单元所占据的已知栖息地类型相对应，包括穴居、沿海洄游、表水层、中层、底栖、深海底栖、共生和礁相关的分类单元。与对单个鱼卵进行条码技术分析相比，代谢条码技术分析鱼卵更快且成本低得多；然而，由于不同分类单元中线粒体 DNA 的拷贝数不同、不同发育阶段的卵内细胞数量不同以及 PCR 扩增偏倚，这种方法不能提供绝对的分类单元比例。此外，一些样本产生的序列比存在的卵数多，这表明存在污染 DNA，需要应用一个阈值，即存在一个分类单元所需的序列比例，才能将其计数。最后，我们综述了使用代谢条码技术和单个鱼卵条码技术进行长期监测计划的优缺点。
