title: Genomic organization of the crested ibis MHC provides new insight into ancestral avian MHC structure.
abstract: The major histocompatibility complex (MHC) plays an important role in immune response. Avian MHCs are not well characterized, only reporting highly compact Galliformes MHCs and extensively fragmented zebra finch MHC. We report the first genomic structure of an endangered Pelecaniformes (crested ibis) MHC containing 54 genes in three regions spanning ~500 kb. In contrast to the loose BG (26 loci within 265 kb) and Class I (11 within 150) genomic structures, the Core Region is condensed (17 within 85). Furthermore, this Region exhibits a COL11A2 gene, followed by four tandem MHC class II αβ dyads retaining two suites of anciently duplicated "αβ" lineages. Thus, the crested ibis MHC structure is entirely different from the known avian MHC architectures but similar to that of mammalian MHCs, suggesting that the fundamental structure of ancestral avian class II MHCs should be "COL11A2-IIαβ1-IIαβ2." The gene structures, residue characteristics, and expression levels of the five class I genes reveal inter-locus functional divergence. However, phylogenetic analysis indicates that these five genes generate a well-supported intra-species clade, showing evidence for recent duplications. Our analyses suggest dramatic structural variation among avian MHC lineages, help elucidate avian MHC evolution, and provide a foundation for future conservation studies.
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Li-Cheng
authors.initials: LC
authors.lastname: Chen
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Hong
authors.initials: H
authors.lastname: Lan
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Li
authors.initials: L
authors.lastname: Sun
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Yan-Li
authors.initials: YL
authors.lastname: Deng
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Ke-Yi
authors.initials: KY
authors.lastname: Tang
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Qiu-Hong
authors.initials: QH
authors.lastname: Wan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001717:Birds / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000378:metabolism; D005091:Exons / Q000235:genetics; D005786:Gene Expression Regulation; D016678:Genome; D023281:Genomics; D015395:Histocompatibility Antigens Class I / Q000737:chemistry / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence; D008285:Major Histocompatibility Complex / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D015395:Histocompatibility Antigens Class I