Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire
Date
2010-10-05
Authors
Quinn, Nicole L.
Boroevich, Keith A.
Lubieniecki, Krysztof P.
Chow, William
Davidson, Evelyn A.
Phillips, Ruth B.
Koop, Benjamin F.
Davidson, William S.
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid
state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model
organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic
and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod
hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost
hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species
for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental
conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure
and organization of the Atlantic salmon a and b hemoglobin genes is of great interest.
Results: We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters
spanning the entire a and b hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal
locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping,
demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and
assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like
genes. This revealed that the tail-to-tail organization and alternating pattern of the a and b hemoglobin genes are
well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin
genes, including non-Bohr b globin genes, than the genomes of other teleosts that have been sequenced.
Conclusions: We suggest that the most parsimonious evolutionary path leading to the present organization of the
Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster after the whole genome
duplication (WGD) at the base of the teleost radiation but prior to the salmonid-specific WGD, which then
produced the duplicated copies seen today. We also propose that the relatively high number of hemoglobin
genes as well as the presence of non-Bohr b hemoglobin genes may be due to the dynamic life history of salmon
and the diverse environmental conditions that the species encounters.
Description
BioMed Central
Keywords
Citation
Quinn et al.: Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire. BMC Genomics 2010 11:539.