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MBE Advance Access published online on August 1, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm158
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© 2007 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Article

Divergence in Expression Between Duplicated Genes in Arabidopsis

Eric W. Ganko1, Blake C. Meyers3 and Todd J. Vision1,2

1 Department of Biology, University of North Carolina at Chapel Hill
3 Department of Plant and Soil Science, University of Delaware

2 Author for correspondence: Campus Box 3280, Department of Biology, University of North Carolina, Chapel Hill, NC 27599, 919.843.4507 (phone), 919.962.1625 (fax), tjv{at}bio.unc.edu (email)

Received for publication April 11, 2007. Revision received July 5, 2007. Accepted for publication July 28, 2007.

New genes may arise through tandem duplication, dispersed small-scale duplication and polyploidy, and patterns of divergence between duplicated genes may vary among these classes. We have examined patterns of gene expression and coding sequence divergence between duplicated genes in Arabidopsis thaliana. Due to the simultaneous origin of polyploidy-derived gene pairs, we can compare covariation in the rates of expression divergence and sequence divergence within this group. Among tandem and dispersed duplicates, much of the divergence in expression profile appears to occur at or shortly after duplication. Contrary to findings from other eukaryotic systems, there is little relationship between expression divergence and synonymous substitutions, while there is a strong positive relationship between expression divergence and nonsynonymous substitutions. Since this pattern is pronounced among the polyploidy-derived pairs, we infer that the strength of purifying selection acting on protein sequence and expression pattern is correlated. The polyploidy-derived pairs are somewhat atypical in that they have broader expression patterns and are expressed at higher levels, suggesting differences among polyploidy and non-polyploidy derived duplicates in the types of genes that revert to single-copy. Finally, within many of the duplicated pairs, one gene is expressed at a higher level across all assayed conditions, which suggests that the subfunctionalization model for duplicate gene preservation provides, at best, only a partial explanation for the patterns of expression divergence between duplicated genes.

Key Words: duplicate gene • subfunctionalization • linkage • MPSS • AtGenExpress • Arabidopsis thaliana


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