PMID- 20923558
OWN - NLM
STAT- MEDLINE
DCOM- 20101227
LR  - 20240416
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 11
DP  - 2010 Oct 5
TI  - Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire.
PG  - 539
LID - 10.1186/1471-2164-11-539 [doi]
AB  - 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 alpha and beta hemoglobin 
      genes is of great interest. RESULTS: We identified four bacterial artificial 
      chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire alpha 
      and beta 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 alpha 
      and beta hemoglobin genes are well conserved in both clusters, as well as that the 
      Atlantic salmon genome houses substantially more hemoglobin genes, including 
      non-Bohr beta 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 beta 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.
FAU - Quinn, Nicole L
AU  - Quinn NL
AD  - Department of Molecular Biology and Biochemistry, Simon Fraser University, 
      Burnaby, British Columbia, Canada.
FAU - Boroevich, Keith A
AU  - Boroevich KA
FAU - Lubieniecki, Krzysztof P
AU  - Lubieniecki KP
FAU - Chow, William
AU  - Chow W
FAU - Davidson, Evelyn A
AU  - Davidson EA
FAU - Phillips, Ruth B
AU  - Phillips RB
FAU - Koop, Ben F
AU  - Koop BF
FAU - Davidson, William S
AU  - Davidson WS
LA  - eng
SI  - GENBANK/GQ898924
SI  - GENBANK/GQ898925
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20101005
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (Hemoglobins)
SB  - IM
MH  - Animals
MH  - Atlantic Ocean
MH  - Chromosome Mapping
MH  - Chromosomes, Artificial, Bacterial/genetics
MH  - Conserved Sequence
MH  - *Evolution, Molecular
MH  - Female
MH  - Gene Order/genetics
MH  - Genetic Linkage
MH  - Genome/*genetics
MH  - Hemoglobins/*genetics
MH  - Karyotyping
MH  - Molecular Sequence Annotation
MH  - Molecular Sequence Data
MH  - Multigene Family
MH  - Phylogeny
MH  - Salmo salar/*genetics
MH  - Synteny/genetics
MH  - Transcription, Genetic
MH  - Xenopus/genetics
PMC - PMC3091688
EDAT- 2010/10/07 06:00
MHDA- 2010/12/28 06:00
PMCR- 2010/10/05
CRDT- 2010/10/07 06:00
PHST- 2010/03/19 00:00 [received]
PHST- 2010/10/05 00:00 [accepted]
PHST- 2010/10/07 06:00 [entrez]
PHST- 2010/10/07 06:00 [pubmed]
PHST- 2010/12/28 06:00 [medline]
PHST- 2010/10/05 00:00 [pmc-release]
AID - 1471-2164-11-539 [pii]
AID - 10.1186/1471-2164-11-539 [doi]
PST - epublish
SO  - BMC Genomics. 2010 Oct 5;11:539. doi: 10.1186/1471-2164-11-539.