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Originally published as Genetics Published Articles Ahead of Print on December 28, 2006.
Genetics, Vol. 175, 1407-1418, March 2007, Copyright © 2007
doi:10.1534/genetics.106.066720
Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species
Zhongying Zhao*,1,
James H. Thomas
,
Nansheng Chen*,
Jonathan A. Sheps
and
David L. Baillie*
* Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada, Department of Genome Sciences, University of Washington, Seattle, Washington 98195 and British Columbia Cancer Research Center, Vancouver, British Columbia V5Z 1L6, Canada
1 Corresponding author: Department of Genome Sciences, University of Washington, Box 355065, 1705 NE Pacific St., Seattle, WA 98195.
E-mail: zyzhao{at}u.washington.edu
ABC transporters constitute one of the largest gene families in all species. They are mostly involved in transport of substrates across membranes. We have previously demonstrated that the Caenorhabditis elegans ABC family shows poor one-to-one gene orthology with other distant model organisms. To address the evolution dynamics of this gene family among closely related species, we carried out a comparative analysis of the ABC family among the three nematode species C. elegans, C. briggsae, and C. remanei. In contrast to the previous observations, the majority of ABC genes in the three species were found in orthologous trios, including many tandemly duplicated ABC genes, indicating that the gene duplication took place before speciation. Species-specific expansions of ABC members are rare and mostly observed in subfamilies A and B. C. briggsae and C. remanei orthologous ABC genes tend to cluster on trees, with those of C. elegans as an outgroup, consistent with their proposed species phylogeny. Comparison of intron/exon structures of the highly conserved ABCE subfamily members also indicates a closer relationship between C. briggsae and C. remanei than between either of these species and C. elegans. A comparison between insect and mammalian species indicates lineage-specific duplications or deletions of ABC genes, while the family size remains relatively constant. Sites undergoing positive selection within subfamily D, which are implicated in very-long-chain fatty acid transport, were identified. The evolution of these sites might be driven by the changes in food source with time.
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