USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA.
USDA-ARS Warmwater Aquaculture Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA.
G3 (Bethesda). 2023 Aug 30;13(9). doi: 10.1093/g3journal/jkad138.
Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North American (N.A.) origin. Given the genetic and genomic differences between the 2 lineages, it is crucial to develop unique genomic resources for N.A. Atlantic salmon. Here, we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole-genome resequencing of 80 N.A. Atlantic salmon individuals. Secondly, a high-density 50K SNP array enriched for the genic regions of the genome and containing 3 sex determination and 61 putative continent of origin markers was developed and validated. Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers was generated from 2,512 individuals in 141 full-sib families. Finally, a chromosome-level de novo genome assembly from a male N.A. Atlantic salmon from the St. John River aquaculture strain was generated using PacBio long reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of the conserved Actinopterygii genes in the assembly, and the genetic linkage information was used to guide the formation of 27 chromosome sequences. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the 2 lineages are caused by a fission in chromosome Ssa01 and 3 chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29, and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species.
北美东北部和加拿大东部的大西洋鲑(Salmo salar)因其在运动钓鱼和水产养殖行业的高经济价值而备受重视。起源于欧洲的大西洋鲑和北美的(N.A.)大西洋鲑之间的基因组存在很大差异。鉴于这两个谱系之间的遗传和基因组差异,为 N.A.大西洋鲑开发独特的基因组资源至关重要。在这里,我们描述了我们最近为 N.A.大西洋鲑水产养殖的基因组和遗传研究开发的资源。首先,我们使用 80 个 N.A.大西洋鲑个体的全基因组重测序数据生成了一个包含 310 万个假定 SNP 的新的 N.A.大西洋鲑单核苷酸多态性(SNP)数据库。其次,开发并验证了一种高密度 50K SNP 阵列,该阵列富集了基因组的基因区域,包含 3 个性别决定和 61 个假定的大陆起源标记。第三,从 141 个全同胞家系的 2512 个个体中生成了由 27 个连锁群组成的遗传图谱,其中包含 36K SNP 标记。最后,使用 PacBio 长读序列从圣约翰河水产养殖品系的雄性 N.A.大西洋鲑中生成了染色体水平的从头基因组组装。Hi-C 接近连接序列和 Bionano 光学图谱的信息用于将 contigs 拼接成 scaffolds。组装包含 1755 个 scaffolds,仅 1253 个 gap,总长度为 2.83Gb,N50 为 17.2Mb。BUSCO 分析检测到组装中 96.2%的保守的辐鳍鱼基因,遗传连锁信息用于指导 27 条染色体序列的形成。与欧洲大西洋鲑参考基因组组装的比较分析证实,这两个谱系之间的染色体差异是由染色体 Ssa01 的裂变以及包括染色体 Ssa01 的 p 臂与 Ssa23、Ssa08 与 Ssa29 以及 Ssa26 与 Ssa28 的 3 条染色体融合引起的。我们为大西洋鲑生成的基因组资源为遗传研究以及该高度重视的物种的养殖和野生种群的管理提供了重要的推动力。