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A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)
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  • Seth Smith,
  • Eric Normandeau,
  • Haig Djambazian,
  • Pubudu Nawarathna,
  • Pierre Berube,
  • Andrew Muir,
  • Jiannis Ragoussis,
  • Chantelle Penney,
  • Kim Scribner,
  • Gordon Luikart,
  • Chris Wilson,
  • Louis Bernatchez
Seth Smith
Michigan State University
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Eric Normandeau
Université Laval
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Haig Djambazian
McGill University
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Pubudu Nawarathna
McGill University
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Pierre Berube
McGill University
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Andrew Muir
Great Lakes Fishery Commission
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Jiannis Ragoussis
McGill University
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Chantelle Penney
Trent University
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Kim Scribner
Michigan State University
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Gordon Luikart
University of Montana
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Chris Wilson
Ontario Ministry of Natural Resources
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Louis Bernatchez
Université Laval
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Abstract

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

Peer review status:IN REVISION

23 Mar 2021Submitted to Molecular Ecology Resources
06 Apr 2021Assigned to Editor
06 Apr 2021Submission Checks Completed
08 Apr 2021Reviewer(s) Assigned
03 May 2021Review(s) Completed, Editorial Evaluation Pending
19 May 2021Editorial Decision: Revise Minor