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Smith SR, Normandeau E, Djambazian H, et al. A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush). Mol Ecol Resour. 2021;doi: 10.1111/1755-0998.13483.
Smith, S. R., Normandeau, E., Djambazian, H., Nawarathna, P. M., Berube, P., Muir, A. M., Ragoussis, J., Penney, C. M., Scribner, K. T., Luikart, G., Wilson, C. C., & Bernatchez, L. (2021). A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush). Molecular ecology resources, . https://doi.org/10.1111/1755-0998.13483
Smith, Seth R, et al. "A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)." Molecular ecology resources vol. (2021). doi: https://doi.org/10.1111/1755-0998.13483
Smith SR, Normandeau E, Djambazian H, Nawarathna PM, Berube P, Muir AM, Ragoussis J, Penney CM, Scribner KT, Luikart G, Wilson CC, Bernatchez L. A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush). Mol Ecol Resour. 2021 Aug 05; doi: 10.1111/1755-0998.13483. Epub 2021 Aug 05. PMID: 34351050.
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Mol Ecol Resour. 2021 Aug 05; doi: 10.1111/1755-0998.13483. Epub 2021 Aug 05.

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

Molecular ecology resources

Seth R Smith, Eric Normandeau, Haig Djambazian, Pubudu M Nawarathna, Pierre Berube, Andrew M Muir, Jiannis Ragoussis, Chantelle M Penney, Kim T Scribner, Gordon Luikart, Chris C Wilson, Louis Bernatchez

Affiliations

  1. Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
  2. Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA.
  3. Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada.
  4. McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada.
  5. Department of Human Genetics, Canadian Centre for Computational Genomics (C3G, McGill University, Montréal, QC, Canada.
  6. Great Lakes Fishery Commission, Ann Arbor, MI, USA.
  7. Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada.
  8. Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.
  9. Fish and Wildlife Genomics Group, University of Montana, Missoula, MT, USA.
  10. Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Polson, MT, USA.
  11. Aquatic Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada.

PMID: 34351050 DOI: 10.1111/1755-0998.13483

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) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual. 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues 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 mitochondrial genome assembly was also produced. Self-versus-self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also allowed us to identify homologous chromosomes in related taxa. 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 data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed.

© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

Keywords: Salvelinus ; Lake Trout; genome assembly; genomics; salmonid

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