GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany.
CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
Genomics. 2020 Nov;112(6):4297-4303. doi: 10.1016/j.ygeno.2020.06.041. Epub 2020 Jul 3.
Extensive fishing has led to fish stock declines throughout the last decades. While clear stock identification is required for designing management schemes, stock delineation is problematic due to generally low levels of genetic structure in marine species. The development of genomic resources can help to solve this issue. Here, we present the first mitochondrial and nuclear draft genome assemblies of three economically important Mediterranean fishes, the white seabream, the striped red mullet, and the comber. The assemblies are between 613 and 785 Mbp long and contain between 27,222 and 32,375 predicted genes. They were used as references to map Restriction-site Associated DNA markers, which were developed with a single-digest approach. This approach provided between 15,710 and 21,101 Single Nucleotide Polymorphism markers per species. These genomic resources will allow uncovering subtle genetic structure, identifying stocks, assigning catches to populations and assessing connectivity. Furthermore, the annotated genomes will help to characterize adaptive divergence.
过去几十年的过度捕捞导致鱼类种群数量减少。虽然明确的种群识别对于设计管理方案是必需的，但由于海洋物种的遗传结构通常较低，种群划分存在问题。基因组资源的开发可以帮助解决这个问题。在这里，我们介绍了三种经济上重要的地中海鱼类——白鲷、条纹红鲻鱼和鲷鱼的第一个线粒体和核基因组草案组装。这些组装的长度在 613 到 785 Mbp 之间，包含 27222 到 32375 个预测基因。它们被用作参考来映射限制性位点相关 DNA 标记，这些标记是通过单消化方法开发的。这种方法为每个物种提供了 15710 到 21101 个单核苷酸多态性标记。这些基因组资源将有助于揭示微妙的遗传结构，识别种群，将捕获物分配给种群并评估连通性。此外，注释基因组将有助于表征适应性分化。
