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Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provides insight into chromosomal evolution and rediploidization across salmonids

Danielle M. Blumstein, Matthew A. Campbell, Matthew C. Hale, View ORCID ProfileBen J. G. Sutherland, View ORCID ProfileGarrett J. McKinney, View ORCID ProfileWendylee Stott, View ORCID ProfileWesley A. Larson
doi: https://doi.org/10.1101/834937
Danielle M. Blumstein
College of Natural Resources, University of Wisconsin-Stevens Point
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Matthew A. Campbell
University of Alaska Museum of the North, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
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Matthew C. Hale
Department of Biology, Texas Christian University, Fort Worth, TX, 76122
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Ben J. G. Sutherland
Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, V9T 6N7, British Columbia, Canada
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  • ORCID record for Ben J. G. Sutherland
Garrett J. McKinney
National Marine Fisheries Service, Northwest Fisheries Science Center
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Wendylee Stott
U.S. Geological Survey, Great Lakes Science Center, Ann Arbor, MI
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  • ORCID record for Wendylee Stott
Wesley A. Larson
U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens PointCollege of Natural Resources, University of Wisconsin-Stevens Point
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  • For correspondence: wlarson@uwsp.edu
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Abstract

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy simultaneously are of particular interest, as understanding the mechanisms that maintain this mosaic of ploidy after WGDs may provide important insights into evolutionary processes. Salmonids are a useful model to study the effect of WGDs due to the extensive diversity that has evolved following an ancestral autotetraploidization event. Although most of the salmonid genome has reverted to diploidy following WGD, approximately 25% of the chromosomes continue to exist in a state of residual tetrasomy. In this study, we generate a novel linkage map for cisco (Coregonus artedi) and conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. Additionally, we propose a new naming strategy, protokaryotypes, that facilitates comparisons across Salmonids by standardizing naming to ancestral chromosomes from northern pike (Esox lucius). The female linkage map for cisco contains 20,450 loci, 3,383 of which are likely contained within residually tetraploid regions of the genome. Comparative genomic analysis revealed that patterns of residual tetrasomy are generally conserved across species, but there is interspecific variation in the relative extent of the residual tetrasomy. Additionally, with the current reference genomes available, we only find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.

Footnotes

  • Data deposition: Raw sequence data has been uploaded to SRA under BioProject PRJNA555579

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 08, 2019.
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Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provides insight into chromosomal evolution and rediploidization across salmonids
Danielle M. Blumstein, Matthew A. Campbell, Matthew C. Hale, Ben J. G. Sutherland, Garrett J. McKinney, Wendylee Stott, Wesley A. Larson
bioRxiv 834937; doi: https://doi.org/10.1101/834937
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Comparative genomic analyses and a novel linkage map for cisco (Coregonus artedi) provides insight into chromosomal evolution and rediploidization across salmonids
Danielle M. Blumstein, Matthew A. Campbell, Matthew C. Hale, Ben J. G. Sutherland, Garrett J. McKinney, Wendylee Stott, Wesley A. Larson
bioRxiv 834937; doi: https://doi.org/10.1101/834937

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