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Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

Miyako Kodama, Marine S. O. Brieuc, Robert H. Devlin, Jeffrey J. Hard and Kerry A. Naish
G3: Genes, Genomes, Genetics Early online July 21, 2014; https://doi.org/10.1534/g3.114.012294
Miyako Kodama
University of Washington;
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Marine S. O. Brieuc
University of Washington;
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Robert H. Devlin
Fisheries and Oceans Canada;
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Jeffrey J. Hard
National Marine Fisheries Service
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Kerry A. Naish
University of Washington;
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Abstract

Whole genome duplication has been implicated in evolutionary innovation and rapid diversification. In salmonid fishes, however, whole genome duplication significantly pre-dates major transitions across the family, and re-diploidization has been a gradual process between genomes that have remained essentially collinear. Nevertheless, pairs of duplicated chromosome arms have diverged at different rates from each other, suggesting that the retention of duplicated regions through occasional pairing between homeologous chromosomes may have played an evolutionary role across species pairs. Extensive chromosomal arm rearrangements have been a key mechanism involved in re-dipliodization of the salmonid genome and so we investigated their influence on degree of differentiation between homeologs across salmon species. We derived a linkage map for coho salmon and performed comparative mapping across syntenic arms within the genus Oncorhynchus, and with the genus Salmo, to determine the phylogenetic relationship between chromosome arrangements and the retention of undifferentiated duplicated regions. A 6596.7cM female coho salmon map, comprising 34 linkage groups with 7415 and 1266 non-duplicated and duplicated loci respectively, revealed uneven distribution of duplicated loci along and between chromosome arms. These duplicated regions were conserved across syntenic arms across Oncorhynchus species, and were identified in metacentric chromosomes likely formed ancestrally to the divergence of Oncorhynchus from Salmo. These findings support earlier studies, where observed pairings involved at least one metacentric chromosomes. Re-diploidization in salmon may have been prevented or retarded by the formation of metacentric chromosomes following the whole genome duplication event, and may explain lineage-specific innovations in salmon species if functional genes are found in these regions.

  • Chromsome rearrangements
  • Comparative genome mapping
  • RAD sequencing
  • Salmon
  • Whole Genome Duplication
  • Received May 22, 2014.
  • Accepted July 13, 2014.
  • Copyright © 2014 Author et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Volume 8 Issue 4, April 2018

G3: Genes|Genomes|Genetics: 8 (4)

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Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

Miyako Kodama, Marine S. O. Brieuc, Robert H. Devlin, Jeffrey J. Hard and Kerry A. Naish
G3: Genes, Genomes, Genetics Early online July 21, 2014; https://doi.org/10.1534/g3.114.012294
Miyako Kodama
University of Washington;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marine S. O. Brieuc
University of Washington;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert H. Devlin
Fisheries and Oceans Canada;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeffrey J. Hard
National Marine Fisheries Service
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kerry A. Naish
University of Washington;
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  • Find this author on PubMed
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  • For correspondence: knaish@uw.edu
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Citation

Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

Miyako Kodama, Marine S. O. Brieuc, Robert H. Devlin, Jeffrey J. Hard and Kerry A. Naish
G3: Genes, Genomes, Genetics Early online July 21, 2014; https://doi.org/10.1534/g3.114.012294
Miyako Kodama
University of Washington;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marine S. O. Brieuc
University of Washington;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert H. Devlin
Fisheries and Oceans Canada;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jeffrey J. Hard
National Marine Fisheries Service
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kerry A. Naish
University of Washington;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: knaish@uw.edu

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