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

被引:50
作者
Kodama, Miyako [1 ]
Brieuc, Marine S. O. [1 ]
Devlin, Robert H. [2 ]
Hard, Jeffrey J. [3 ]
Naish, Kerry A. [1 ]
机构
[1] Univ Washington, Sch Aquat & Fishery Sci, Seattle, WA 98105 USA
[2] Fisheries & Oceans Canada, W Vancouver, BC V7K 1N6, Canada
[3] NOAA, Natl Marine Fisheries Serv, NW Fisheries Sci Ctr, Seattle, WA 98112 USA
来源
G3-GENES GENOMES GENETICS | 2014年 / 4卷 / 09期
关键词
chromsome rearrangements; comparative genome mapping; RAD sequencing; salmon; whole genome duplication; RAINBOW-TROUT GENOME; ATLANTIC SALMON; LINKAGE MAP; GENE DUPLICATION; SEGREGATION DISTORTION; ARCTIC CHARR; EVOLUTION; REVEALS; SALAR; CONSERVATION;
D O I
10.1534/g3.114.012294
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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; therefore, 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 6596.7 cM female coho salmon map, comprising 30 linkage groups with 7415 and 1266 nonduplicated 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 previous studies in which observed pairings involved at least one metacentric chromosome. Re-diploidization in salmon may have been prevented or retarded by the formation of metacentric chromosomes after the whole genome duplication event and may explain lineage-specific innovations in salmon species if functional genes are found in these regions.
引用
收藏
页码:1717 / 1730
页数:14
相关论文
共 78 条
  • [1] Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae
    Alexandrou, Markos A.
    Swartz, Brian A.
    Matzke, Nicholas J.
    Oakley, Todd H.
    [J]. MOLECULAR PHYLOGENETICS AND EVOLUTION, 2013, 69 (03) : 514 - 523
  • [2] Allendorf F.W., 1984, P1
  • [3] Allendorf FW, 1997, GENETICS, V145, P1083
  • [4] BASIC LOCAL ALIGNMENT SEARCH TOOL
    ALTSCHUL, SF
    GISH, W
    MILLER, W
    MYERS, EW
    LIPMAN, DJ
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
  • [5] [Anonymous], 2007, The Origins of Genome Architecture
  • [6] [Anonymous], 2013, R LANG ENV STAT COMP
  • [7] Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
    Baird, Nathan A.
    Etter, Paul D.
    Atwood, Tressa S.
    Currey, Mark C.
    Shiver, Anthony L.
    Lewis, Zachary A.
    Selker, Eric U.
    Cresko, William A.
    Johnson, Eric A.
    [J]. PLOS ONE, 2008, 3 (10):
  • [8] The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates
    Berthelot, Camille
    Brunet, Frederic
    Chalopin, Domitille
    Juanchich, Amelie
    Bernard, Maria
    Noel, Benjamin
    Bento, Pascal
    Da Silva, Corinne
    Labadie, Karine
    Alberti, Adriana
    Aury, Jean-Marc
    Louis, Alexandra
    Dehais, Patrice
    Bardou, Philippe
    Montfort, Jerome
    Klopp, Christophe
    Cabau, Cedric
    Gaspin, Christine
    Thorgaard, Gary H.
    Boussaha, Mekki
    Quillet, Edwige
    Guyomard, Rene
    Galiana, Delphine
    Bobe, Julien
    Volff, Jean-Nicolas
    Genet, Carine
    Wincker, Patrick
    Jaillon, Olivier
    Roest Crollius, Hugues
    Guiguen, Yann
    [J]. NATURE COMMUNICATIONS, 2014, 5
  • [9] SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
    Bourret, Vincent
    Kent, Matthew P.
    Primmer, Craig R.
    Vasemagi, Anti
    Karlsson, Sten
    Hindar, Kjetil
    Mcginnity, Philip
    Verspoor, Eric
    Bernatchez, Louis
    Lien, Sigbjorn
    [J]. MOLECULAR ECOLOGY, 2013, 22 (03) : 532 - 551
  • [10] A Dense Linkage Map for Chinook salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event
    Brieuc, Marine S. O.
    Waters, Charles D.
    Seeb, James E.
    Naish, Kerry A.
    [J]. G3-GENES GENOMES GENETICS, 2014, 4 (03): : 447 - 460