MHC Class II Pseudogene and Genomic Signature of a 32-kb Cosmid in the House Finch (Carpodacus mexicanus)

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Abstract
Large-scale sequencing studies in vertebrates have thus far focused primarily on the genomes of a few model organisms. Birds are of interest to genomics because of their much smaller and highly streamlined genomes compared to mammals. However, large-scale genetic work has been confined almost exclusively to the chicken; we know little about general aspects of genomes in nongame birds. This study examines the organization of a genomic region containing anMhcclass II B gene in a representative of another important lineage of the avian tree, the songbirds (Passeriformes). We used a shotgun sequencing approach to determine the sequence of a 32-kb cosmid insert containing a strongly hybridizingMhcfragment from house finches (Carpodacus mexicanus). There were a total of three genes found on the cosmid clone, about the gene density expected for the mammalianMhc: a class IIMhcβ-chain gene (Came–DAB1), a serine–threonine kinase, and a zinc finger motif. Frameshift mutations in both the second and third exons ofCame–DAB1and the unalignability of the gene after the third exon suggest that it is a nonfunctional pseudogene. In addition, the identifiable introns ofCame–DAB1are more than twice as large as those of chickens. Nucleotide diversity in the peptide-binding region ofCame–DAB1(Π = 0.03) was much lower than polymorphic chicken and other functionalMhcgenes but higher than the expected diversity for a neutral locus in birds, perhaps because of hitchhiking on a selectedMhclocus close by. The serine–threonine kinase gene is likely functional, whereas the zinc finger motif is likely nonfunctional. A paucity of long simple-sequence repeats and retroelements is consistent with emerging rules of chicken genomics, and a pictorial analysis of the “genomic signature” of this sequence, the first of its kind for birds, bears strong similarity to mammalian signatures, suggesting common higher-order structures in these homeothermic genomes. The house finch sequence is among a very few of its kind from nonmodel vertebrates and provides insight into the evolution of the avianMhcand of avian genomes generally.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF205032andAF241546–AF241565.]