title: A 39-kb sequence around a blackbird Mhc class II gene: ghost of selection past and songbird genome architecture.
abstract: To gain an understanding of the evolution and genomic context of avian major histocompatibility complex (Mhc) genes, we sequenced a 38.8-kb Mhc-bearing cosmid insert from a red-winged blackbird (Agelaius phoeniceus). The DNA sequence, the longest yet retrieved from a bird other than a chicken, provides a detailed view of the process of gene duplication, divergence, and degeneration ("birth and death") in the avian Mhc, as well as a glimpse into major noncoding features of a songbird genome. The peptide-binding region (PBR) of the single Mhc class II B gene in this region, Agph-DAB2, is almost devoid of polymorphism, and a still-segregating single-base-pair deletion and other features suggest that it is nonfunctional. Agph-DAB2 is estimated to have diverged about 40 MYA from a previously characterized and highly polymorphic blackbird Mhc gene, Aph-DAB1, and is therefore younger than most mammalian Mhc paralogs and arose relatively late in avian evolution. Despite its nonfunctionality, Agph-DAB2 shows very high levels of nonsynonymous divergence from Agph-DAB1 and from reconstructed ancestral sequences in antigen-binding PBR codons-a strong indication of a period of adaptive divergence preceding loss of function. We also found that the region sequenced contains very few other unambiguous genes, a partial Mhc- class II gene fragment, and a paucity of simple-sequence and other repeats. Thus, this sequence exhibits some of the genomic streamlining expected for avian as compared with mammalian genomes, but is not as densely packed with functional genes as is the chicken Mhc.
authors.affiliation: Department of Zoology, University of Washington, Seatle, WA 98195, USA. sedwards@u.washington.edu
authors.forename: S V
authors.initials: SV
authors.lastname: Edwards
authors.forename: J
authors.initials: J
authors.lastname: Gasper
authors.forename: D
authors.initials: D
authors.lastname: Garrigan
authors.forename: D
authors.initials: D
authors.lastname: Martindale
authors.forename: B F
authors.initials: BF
authors.lastname: Koop
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001717:Birds / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D005796:Genes / Q000235:genetics; D005802:Genes, MHC Class II / Q000235:genetics*; D014644:Genetic Variation; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D020033:Protein Isoforms / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: D020033:Protein Isoforms; D004247:DNA