TY - JOUR
T1 - Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species
AU - Zhao, Zhongying
AU - Thomas, James H
AU - Chen, Nansheng
AU - Sheps, Jonathan A
AU - Baillie, David L
N1 - Funding information:
We thank The Genome Sequencing Center at Washington University in Saint Louis and the Sanger Centre for permission to use the C. briggsae and C. remanei sequence. And we thank Andy Fire for the GFP vector and Ann Rose for dpy-5 mutants and rescue plasmid DNA. All the knockout mutant strains were generated by the C. elegans Knockout Consortium, which is funded by Genome Canada. Several strains were provided by the C. elegans Genetic Center, which is funded by the National Institutes of Health National Center for Research Resources. This work was supported by the Natural Sciences and Engineering Research Council of Canada, Genome British Columbia, and Genome Canada.
Publisher copyright:
© 2007 by the Genetics Society of America
PY - 2007/3/1
Y1 - 2007/3/1
N2 - 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.
AB - 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.
UR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-34249037676&doi=10.1534%2fgenetics.106.066720&partnerID=40&md5=a80252c8823d8f0d43e7ccc1eb88231f
U2 - 10.1534/genetics.106.066720
DO - 10.1534/genetics.106.066720
M3 - Journal article
C2 - 17194779
SN - 0016-6731
VL - 175
SP - 1407
EP - 1418
JO - Genetics
JF - Genetics
IS - 3
ER -