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MBE Advance Access published online on September 26, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn207
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Genome Size Reduction in the Chicken has Involved Massive Loss of Ancestral Protein-Coding Genes

Austin L. Hughes* and Robert Friedman

Department of Biological Sciences, University of South Carolina, Columbia SC 29208 USA

* Author for correspondence at Department of Biological Sciences, Coker Life Sciences Building, 715 Sumter St., University of South Carolina, Columbia SC 29208 USA. Email: austin{at}biol.sc.edu. Tel. : 1-803-777-9186. Fax: 1-803-777-4002.

Received for publication June 2, 2008. Revision received August 15, 2008. Accepted for publication September 12, 2008.

Both mean genomes size and the variance in genome size among species are smaller on average in birds (class Aves) than in the other tetrapod classes. In order to test whether loss of protein-coding genes has contributed to genome size reduction in birds, we compared the chicken genome and five mammalian genomes. Numbers of members (paralogs) were significantly lower in the chicken gene families than in the corresponding mammalian families. Phylogenetic analyses of chicken, mammal, and fish paralogs supported the hypothesis that chicken-specific loss of paralogs occurred much more frequently than mammal-specific gene duplications. Moreover, the phylogenetic analyses supported the hypothesis that a substantial majority of the paralogs lost in chicken originiated from duplications prior to the most recent common ancestor of tetrapods and bony fishes. In addition to loss of paralogs, numerous gene families present in the mammalian genomes were missing in the chicken genome; over 1000 of these families were found in bony fishes, implying presence of the family in the tetrapod ancestor. In the set of families with more members on average in mammals than in the chicken, immune system function was associated with a greater degree of gene family size reduction in the chicken, consistent with other evidence that immune system gene families have become particularly compact in birds.

Key Words: evolution of birds • gene deletion • gene duplication • genome size • immune system genes


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