Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)
Date
2008-11-25
Authors
Danzmann, Roy G
Davidson, Evelyn A
Ferguson, Moira M
Gharbi, Karim
Koop, Ben F
Hoyheim, Bjorn
Lien, Sigbjorn
Lubieniecki, Krzysztof P
Moghadam, Hooman K
Park, Jay
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: 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-rayfinned
fish karyotype in Atlantic salmon and rainbow trout based upon their comparative syntenies
with two model species of 3R ray-finned fishes.
Results: 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.
Conclusion: 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.
Description
BioMed Central
Keywords
Citation
Danzmann et al.: Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon). BMC Genomics 2008, 9:557