Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar)
Date
2007-07-25
Authors
Lukacs, Morten F
Harstad, Håvard
Grimholt, Unni
Beetz-Sargent, Marianne
Cooper, Glenn A
Reid, Linda
Bakke, Hege G.
Phillips, Ruth B
Miller, Kristina M
Davidson, William S
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: We have previously identified associations between major histocompatibility complex
(MHC) class I and resistance towards bacterial and viral pathogens in Atlantic salmon. To evaluate if only
MHC or also closely linked genes contributed to the observed resistance we ventured into sequencing of
the duplicated MHC class I regions of Atlantic salmon.
Results: Nine BACs covering more than 500 kb of the two duplicated MHC class I regions of Atlantic
salmon were sequenced and the gene organizations characterized. Both regions contained the proteasome
components PSMB8, PSMB9, PSMB9-like and PSMB10 in addition to the transporter for antigen processing
TAP2, as well as genes for KIFC1, ZBTB22, DAXX, TAPBP, BRD2, COL11A2, RXRB and SLC39A7. The
IA region contained the recently reported MHC class I Sasa-ULA locus residing approximately 50 kb
upstream of the major Sasa-UBA locus. The duplicated class IB region contained an MHC class I locus
resembling the rainbow trout UCA locus, but although transcribed it was a pseudogene. No other MHC
class I-like genes were detected in the two duplicated regions. Two allelic BACs spanning the UBA locus
had 99.2% identity over 125 kb, while the IA region showed 82.5% identity over 136 kb to the IB region.
The Atlantic salmon IB region had an insert of 220 kb in comparison to the IA region containing three
chitin synthase genes.
Conclusion: We have characterized the gene organization of more than 500 kb of the two duplicated
MHC class I regions in Atlantic salmon. Although Atlantic salmon and rainbow trout are closely related,
the gene organization of their IB region has undergone extensive gene rearrangements. The Atlantic
salmon has only one class I UCA pseudogene in the IB region while trout contains the four MHC UCA, UDA,
UEA and UFA class I loci. The large differences in gene content and most likely function of the salmon and
trout class IB region clearly argues that sequencing of salmon will not necessarily provide information
relevant for trout and vice versa.
Description
BioMed Central
Keywords
Citation
Lukacs et al. Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). BMC Genomics 2007, 8 :25