A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)

• DOI: 10.22541/au.161792605.50398568/v1
• Publication Date: 2021-04-08T23:55:00Z
• Authors: Seth Smith; Eric Normandeau; Haig Djambazian; Pubudu Nawarathna; Pierre Berube; Andrew Muir; Jiannis Ragoussis; Chantelle Penney; Kim Scribner; Gordon Luikart; Chris Wilson; Louis Bernatchez
• Keywords: Sequence assembly; Synteny

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and excellent model research on adaptation speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina proximity ligation (Hi-C), previously published linkage map to produce contiguous composed 7,378 contigs (contig N50 = 1.8 mb) assigned 4,120 scaffolds (scaffold 44.975 mb). 84.7% the was 42 chromosome-sized 93.2% Benchmarking Universal Single Copy Orthologs were recovered, putting this par with best currently available genomes. Estimates size based k-mer frequency analysis similar total finished genome, suggesting that entirety recovered. A mitome also produced. Self-vs-self synteny allowed us identify homeologs resulting from Salmonid specific autotetraploid event (Ss4R) alignment three other homologous chromosomes in species. generated multiple resources useful future genomic including repeat library sex averaged recombination map. novel RNA sequencing dataset used publicly set gene annotations using National Center Biotechnology Information Eukaryotic Genome Annotation Pipeline. Potential applications these population genetics native populations are discussed.