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

• Christopher M. Hess

• Joe Gasper

• Hopi E. Hoekstra

• Christopher E. Hill

• Scott V. Edwards

抄録

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 an Mhc class 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 hybridizing Mhc fragment from house finches ( Carpodacus mexicanus ). There were a total of three genes found on the cosmid clone, about the gene density expected for the mammalian Mhc : a class II Mhc β-chain gene ( Came–DAB1 ), a serine–threonine kinase, and a zinc finger motif. Frameshift mutations in both the second and third exons of Came–DAB1 and the unalignability of the gene after the third exon suggest that it is a nonfunctional pseudogene. In addition, the identifiable introns of Came–DAB1 are more than twice as large as those of chickens. Nucleotide diversity in the peptide-binding region of Came–DAB1 (Π = 0.03) was much lower than polymorphic chicken and other functional Mhc genes but higher than the expected diversity for a neutral locus in birds, perhaps because of hitchhiking on a selected Mhc locus 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 avian Mhc and of avian genomes generally. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos.<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="AF205032" ext-link-type="gen" xlink:type="simple">AF205032 and<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="AF241546" ext-link-type="gen" xlink:type="simple">AF241546 –<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="AF241565" ext-link-type="gen" xlink:type="simple">AF241565 .]

収録刊行物

• Genome Research

  Genome Research 10 (5), 613-623, 2000-05-01

  Cold Spring Harbor Laboratory

キーワード

• Genetics (clinical)
• Genetics

詳細情報

• CRID: 1361699995782566528
• NII論文ID: 30018929409
• DOI: 10.1101/gr.10.5.613
• ISSN: 15495469
• ISSN: 10889051
• Web Site: https://syndication.highwire.org/content/doi/10.1101/gr.10.5.613
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