| Summary: | Background: Comparative genomic studies suggest that the modern day assemblage of ray-finnedfishes have descended from an ancestral grouping of fishes that possessed 12–13 linkage groups. Alljawed vertebrates are postulated to have experienced two whole genome duplications (WGD) intheir ancestry (2R duplication). Salmonids have experienced one additional WGD (4R duplicationevent) compared to most extant teleosts which underwent a further 3R WGD compared to othervertebrates. We describe the organization of the 4R chromosomal segments of the proto-rayfinnedfish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenieswith two model species of 3R ray-finned fishes.Results: Evidence is presented for the retention of large whole-arm affinities between theancestral linkage groups of the ray-finned fishes, and the 50 homeologous chromosomal segmentsin Atlantic salmon and rainbow trout. In the comparisons between the two salmonid species, thereis also evidence for the retention of large whole-arm homeologous affinities that are associatedwith the retention of duplicated markers. Five of the 7 pairs of chromosomal arm regionsexpressing the highest level of duplicate gene expression in rainbow trout share homologoussynteny 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.Conclusion: Two chromosome arms in Danio rerio and Oryzias latipes (descendants of the 3Rduplication) 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 supporta 13 proto-linkage group model, and suggest that a 12 proto-linkage group arrangement (i.e., aseparate single chromosome duplication and ancestral fusion/fissions/recombination within theputative G/H/I groupings) may have occurred in the more basal soft-rayed fishes. We also foundevidence supporting the model that ancestral linkage group M underwent a single chromosomeduplication following the 3R duplication. In the salmonids, the M ancestral linkage groups arelocalized to 5 whole arm, and 3 partial arm regions (i.e., 6 whole arm regions expected). Thus, 3distinct ancestral linkage groups are postulated to have existed in the G/H and M lineagechromosomes in the ancestor of the salmonids.
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