Codon usage bias and base composition in MHC genes in humans and common chimpanzees |
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Authors: | S K McWeeney Ana Maria Valdes |
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Institution: | (1) Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California at Berkeley, Berkeley, CA 94720–3140, USA, E-mail: shannon@allele5.biol.berkeley.edu, Tel.: +1-510-6421233, Fax: +1-510-6435144, US |
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Abstract: | Codon bias and base composition in major histocompatibility complex (MHC) sequences have been studied for both class I and
II loci in Homo sapiens and Pan troglodytes. There is low to moderate codon bias for the MHC of humans and chimpanzees. In the class I loci, the same level of moderate
codon bias is seen for HLA-B, HLA-C, Patr-A, Patr-B, and Patr-C, while at HLA-A the level of codon bias is lower. There is a correlation between codon usage bias and G+C content in the A and B loci in humans and chimps, but not at the C locus. To examine the effect of diversifying selection on codon bias, we subdivided class I alleles into antigen recognition
site (ARS) and non-ARS codons. ARS codons had lower bias than non-ARS codons. This may indicate that the constraint of codon
bias on nucleotide substitution may be selected against in ARS codons. At the class II loci, there are distinct differences
between alpha and beta chain genes with respect to codon usage, with the beta chain genes being much more biased. Species-specific
differences in base composition were seen in exon 2 at the DRB1 locus, with lower GC content in chimpanzees. Considering the complex evolutionary history of MHC genes, the study of codon
usage patterns provides us with a better understanding of both the evolutionary history of these genes and the evolution of
synonymous codon usage in genes under natural selection.
Received: 2 April 1998 / Revised: 2 September 1998 |
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Keywords: | MHC Codon usage bias Scaled chi-square Effective number of codons GC content |
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