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.