Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

BMC Genomics

Research Article

Ruth B Phillips¹  Ben F Koop²  William Chow³  Nicole L Quinn³  William S Davidson³  Keith A Boroevich³  Evelyn A Davidson³  Krzysztof P Lubieniecki³ 

[1] Department of Biological Sciences, Washington State University, Vancouver, WA, USA;Department of Biology, University of Victoria, Victoria, British Columbia, Canada;Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada;

关键词: Bacterial Artificial Chromosome;    Atlantic Salmon;    Bacterial Artificial Chromosome Clone;    Bacterial Artificial Chromosome Library;    Whole Genome Duplication;   

DOI  :  10.1186/1471-2164-11-539

 received in 2010-03-19, accepted in 2010-10-05,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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 α and β hemoglobin genes is of great interest.ResultsWe identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β 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 α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced.ConclusionsWe 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 β hemoglobin genes may be due to the dynamic life history of salmon and the diverse environmental conditions that the species encounters.Data deposition: BACs S0155C07 and S0079J05 (fps135): GenBank GQ898924; BACs S0055H05 and S0014B03 (fps1046): GenBank GQ898925

【 授权许可】

Unknown   
© Quinn et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.