Salmo salar strain:St. John River | breed:North American Atlantic salmon Genome sequencing and assembly

The North American (N.A.) Atlantic salmon is a sub-species of Atlantic salmon with substantial genomic differences from the European sub-species of the same species. A high quality reference de-novo assembly is needed for the N.A. Atlantic salmon. To accomplish this, we generated 104x genome coverage of PacBio RS-II long-read sequences with a male N.A. Atlantic salmon from the St. John River broodstock of the USDA breeding program in Maine, USA. Contigs were assembled from the long reads using the Canu pipeline. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 1,755 scaffolds. The scaffolds were polished using the PacBio raw reads and ~132x Illumina short reads. A genetic map composed of 27 linkage groups was generated from 36K SNP markers and 2,512 fish from 141 full-sib families. The genetic linkage information was used to anchor the scaffolds to 27 chromosomes and to order and orient the scaffold sequences in the chromosome sequences.

北美大西洋鲑（北美N.A.大西洋鲑）是该物种的亚种，其基因组与欧洲亚种存在显著差异。为北美大西洋鲑构建一个高质量的参考从头组装（de-novo assembly）是必要的。为此，我们利用来自美国缅因州圣约翰河流域的USDA育种项目中的雄性北美大西洋鲑，生成了PacBio RS-II长读长序列的104倍基因组覆盖率。通过Canu管道从长读长中组装得到连续片段（contigs）。进一步利用Bionano光学图谱和Hi-C邻近连接序列数据，对组装结果进行优化，生成了1,755个支架（scaffolds）。使用PacBio原始读长和约132倍Illumina短读长对支架进行抛光。从36K个单核苷酸多态性（SNP）标记和141个全同胞家系中的2,512尾鱼中构建了一个包含27个连锁群的遗传图谱。利用遗传连锁信息将支架锚定到27条染色体上，并在染色体序列中排列和定向支架序列。