title: Sequencing and comparative analysis of the gorilla MHC genomic sequence.
abstract: Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Laurens G
authors.initials: LG
authors.lastname: Wilming
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Hart
authors.forename: Penny C
authors.initials: PC
authors.lastname: Coggill
authors.forename: Roger
authors.initials: R
authors.lastname: Horton
authors.forename: James G R
authors.initials: JG
authors.lastname: Gilbert
authors.forename: Chris
authors.initials: C
authors.lastname: Clee
authors.forename: Matt
authors.initials: M
authors.lastname: Jones
authors.forename: Christine
authors.initials: C
authors.lastname: Lloyd
authors.forename: Sophie
authors.initials: S
authors.lastname: Palmer
authors.forename: Sarah
authors.initials: S
authors.lastname: Sims
authors.forename: Siobhan
authors.initials: S
authors.lastname: Whitehead
authors.forename: David
authors.initials: D
authors.lastname: Wiley
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Harrow
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D016678:Genome / Q000235:genetics*; D006071:Gorilla gorilla / Q000235:genetics* / Q000276:immunology*; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D002679:Pan troglodytes / Q000235:genetics; D017422:Sequence Analysis, DNA