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

  1. Christopher M. Hess,
  2. Joe Gasper,
  3. Hopi E. Hoekstra,
  4. Christopher E. Hill, and
  5. Scott V. Edwards1
  1. Department of Zoology, University of Washington, Seattle, Washington 98195 USA

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 anMhc 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.AF205032 and AF241546AF241565.]

Footnotes

  • 1 Corresponding author.

  • E-MAIL edwards{at}zoology.washington.edu; FAX (206) 543-3041.

    • Received August 4, 1999.
    • Accepted February 25, 2000.
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