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Open Access Research article

Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)

Roy G Danzmann1, Evelyn A Davidson2, Moira M Ferguson1, Karim Gharbi3, Ben F Koop4, Bjorn Hoyheim5, Sigbjorn Lien67, Krzysztof P Lubieniecki2, Hooman K Moghadam1, Jay Park2, Ruth B Phillips8 and William S Davidson2*

Author Affiliations

1 Department of Integrative Biology, University of Guelph, Guelph, ON Canada, N1G 2W1

2 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby BC, Canada, V5A 1S6

3 Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow, Scotland, UK, G61 1QH

4 Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria BC, Canada,V8W 3N5

5 Norwegian School of Veterinary Science, BasAM-Genetics, Oslo, Norway, NO-0033

6 CIGENE – Centre of Integrative Genetics, Ås, Norway, NO-1432

7 Institute of Animal and Aquacultural Sciences, Norwegian University of Life Science, Ås, Norway, NO-1432

8 School of Biological Sciences, Washington State University, Vancouver, WA USA, 98686-9600

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BMC Genomics 2008, 9:557  doi:10.1186/1471-2164-9-557

Published: 25 November 2008



Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12–13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD) in their ancestry (2R duplication). Salmonids have experienced one additional WGD (4R duplication event) compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates. We describe the organization of the 4R chromosomal segments of the proto-ray-finned fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies with two model species of 3R ray-finned fishes.


Evidence is presented for the retention of large whole-arm affinities between the ancestral linkage groups of the ray-finned fishes, and the 50 homeologous chromosomal segments in Atlantic salmon and rainbow trout. In the comparisons between the two salmonid species, there is also evidence for the retention of large whole-arm homeologous affinities that are associated with the retention of duplicated markers. Five of the 7 pairs of chromosomal arm regions expressing the highest level of duplicate gene expression in rainbow trout share homologous synteny to the 5 pairs of homeologs with the greatest duplicate gene expression in Atlantic salmon. These regions are derived from proto-Actinopterygian linkage groups B, C, E, J and K.


Two chromosome arms in Danio rerio and Oryzias latipes (descendants of the 3R duplication) can, in most instances be related to at least 4 whole or partial chromosomal arms in the salmonid species. Multiple arm assignments in the two salmonid species do not clearly support a 13 proto-linkage group model, and suggest that a 12 proto-linkage group arrangement (i.e., a separate single chromosome duplication and ancestral fusion/fissions/recombination within the putative G/H/I groupings) may have occurred in the more basal soft-rayed fishes. We also found evidence supporting the model that ancestral linkage group M underwent a single chromosome duplication following the 3R duplication. In the salmonids, the M ancestral linkage groups are localized to 5 whole arm, and 3 partial arm regions (i.e., 6 whole arm regions expected). Thus, 3 distinct ancestral linkage groups are postulated to have existed in the G/H and M lineage chromosomes in the ancestor of the salmonids.