title: ERVK9, transposons and the evolution of MHC class I duplicons within the alpha-block of the human and chimpanzee.
abstract: The genomic sequences within the alpha-block (approximately 288-310 kb) of the human and chimpanzee MHC class I region contains ten MHC class I genes and three MIC gene fragments grouped together within alternating duplicated genomic segments or duplicons. In this study, the chimpanzee and human genomic sequences were analyzed in order to determine whether the remnants of the ERVK9 and other retrotransposon sequences are useful genomic markers for reconstructing the evolutionary history of the duplicated MHC gene families within the alpha-block. A variety of genes, pseudogenes, autologous DNA transposons and retrotransposons such as Alu and ERVK9 were used to categorize the ten duplicons into four distinct structural groups. The phylogenetic relationship of the ten duplicons was examined by using the neighbour joining method to analyze transposon sequence topologies of selected Alu members, LTR16B and Charlie9. On the basis of these structural groups and the phylogeny of the duplicated transposon sequences, a duplication model was reconstructed involving four multipartite tandem duplication steps to explain the organization and evolution of the ten duplicons within the alpha-block of the chimpanzee and human. The phylogenetic analysis and inferred duplication history suggests that the Patr/HLA-F was the first MHC class I gene to have been fixed and not required as a precursor for further duplication within the alpha-block of the ancestral species.
authors.affiliation: Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch University, Murdoch, Western Australia. jkulski@murdoch.edu.au
authors.forename: J K
authors.initials: JK
authors.lastname: Kulski
authors.forename: T
authors.initials: T
authors.lastname: Anzai
authors.forename: H
authors.initials: H
authors.lastname: Inoko
mesh_terms: D000818:Animals; D002503:Centromere / Q000235:genetics; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D020440:Gene Duplication; D020131:Genes, Duplicate; D006680:HLA Antigens / Q000235:genetics; D015395:Histocompatibility Antigens Class I / Q000235:genetics*; D006801:Humans; D008285:Major Histocompatibility Complex; D005810:Multigene Family; D002679:Pan troglodytes; D010802:Phylogeny; D018626:Retroelements; D016615:Telomere / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D006680:HLA Antigens; C062341:HLA-F antigens; D015395:Histocompatibility Antigens Class I; D018626:Retroelements