ArticleG3 (Bethesda, Md.)2023
The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon.
Article in G3 (Bethesda, Md.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 22 citations in OpenAlex.
- A Genome-Wide Association Study Identifies Candidate SNPs and Genes Associated with Body Weight in the Northern Snakehead (Animals : an open access journal from MDPI · 2026Article
- The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.Molecular ecology · 2025Review
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Parallel Selection in Domesticated Atlantic Salmon from Divergent Founders Including on Whole-Genome Duplication-derived Homeologous Regions.Genome biology and evolution · 2025Article
- High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.Genetics, selection, evolution : GSE · 2025Article
- Application of genomic tools to study and potentially improve the upper thermal tolerance of farmed Atlantic salmon (Salmo salar).BMC genomics · 2025Article
- Article
- Candidate genes associated with fatty acid compositions in north American Atlantic salmon (Salmo salar).BMC genomics · 2024Article
- A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg.Scientific data · 2024Article
- Genome-wide association identifies genomic regions influencing fillet color in Northwest Atlantic salmon (Frontiers in genetics · 2024Article
- The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon.G3 (Bethesda, Md.) · 2023Article
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Authors and funding
17 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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