title: Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.
abstract: The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Weerachai
authors.initials: W
authors.lastname: Jaratlerdsiri
authors.affiliation: Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia; Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia.
authors.forename: Janine
authors.initials: J
authors.lastname: Deakin
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, United States of America; Department of Genetics, Harvard Medical School, 77 Louis Pasteur Ave., Boston, Massachusetts 02115, United States of America.
authors.forename: Ricardo M
authors.initials: RM
authors.lastname: Godinez
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America.
authors.forename: Xueyan
authors.initials: X
authors.lastname: Shan
authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Peterson
authors.affiliation: Animal Genetics and Integrative Biology, INRA, UMR 1313 Jouy-en-Josas 78352, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Marthey
authors.affiliation: School of Plant Science, University of Arizona, Tucson, Arizona 85721, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States of America.
authors.forename: Fiona M
authors.initials: FM
authors.lastname: McCarthy
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia; Center for Crocodile Research, P.O. Box 329, Noonamah, Northern Territory 0837, Australia.
authors.forename: Sally R
authors.initials: SR
authors.lastname: Isberg
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Damien P
authors.initials: DP
authors.lastname: Higgins
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Amanda Y
authors.initials: AY
authors.lastname: Chong
authors.affiliation: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States of America.
authors.forename: John St
authors.initials: JS
authors.lastname: John
authors.affiliation: Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602, United States of America.
authors.forename: Travis C
authors.initials: TC
authors.lastname: Glenn
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America; Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Jaime
authors.initials: J
authors.lastname: Gongora
mesh_terms: D000489:Alligators and Crocodiles / Q000235:genetics* / Q000821:virology; D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D020451:Contig Mapping; D005805:Genes, MHC Class I / Q000235:genetics*; D005802:Genes, MHC Class II / Q000235:genetics*; D023281:Genomics; D018626:Retroelements / Q000235:genetics; D012190:Retroviridae / Q000235:genetics; D013045:Species Specificity
chemical_list: D018626:Retroelements