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Supplemental Material for Gao et al., 2023

posted on 2023-06-13, 12:51 authored by Guangtu Gao, Geoffrey C. Waldbieser, Ramey C. Youngblood, Dongyan Zhao, Michael R. Pietrak, Melissa S. Allen, Jason A. Stannard, John T. Buchanan, Roseanna L. Long, Melissa Milligan, Gary Burr, Katherine Mejía-Guerra, Moira J. Sheehan, Brian E. Scheffler, Caird E. Rexroad III, Brian C. Peterson, Yniv Palti


File S1: New database of ~2.3M uniquely mapped SNPs generated for N.A. Atlantic salmon including chromosome positions and alternative alleles. (Available to download from GSA journals Figshare and from Github: S1 - DB SNPs

File S2: Linkage map of north American Atlantic salmon from the St. John River aquaculture strain.

File S3: Genome positions of the 50K SNPs included in Axiom high-density SNP array.

File S4: DNA sequence alignments between the Atlantic salmon chromosomes from the north American lineage genome assembly (this report; accession GCA_021399835.1) and the European lineage reference genome assembly (Ssal_v3.1; GCA_905237065.2).


Figure S1. Distribution of markers from the N.A. Atlantic salmon Axiom 50K SNP array on the genome assembly chromosomes. 

Figure S2. A typical linear alignment between chromosome sequences from the N.A. and European Atlantic salmon genomes is shown for chromosome Ssa15. Sequences were compared using data from the reference assembly for the European lineage in NCBI (Ssal_v3.1; GCA_905237065.2).


Article title

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

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