Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

• Published in: BMC Genomics
• Main Authors: Quinn, Nicole L., Boroevich, Keith A., Lubieniecki, Krysztof P., Chow, William, Davidson, Evelyn A., Phillips, Ruth B., Koop, Benjamin F., Davidson, William S.
• Format: Article in Journal/Newspaper
• Language: English
• Published: BioMed Central 2010
• Subjects: Atlantic salmon
• Online Access: http://hdl.handle.net/1828/4995; http://www.biomedcentral.com/1471-2164/11/539; https://doi.org/10.1186/1471-2164-11-539

BioMed Central 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 ...