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Published online on February 8, 2006, 10.1073/pnas.0507782103

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Evolution
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication

( amino acid substitution | Arabidopsis | Oryza | protein functional domain | single-nucleotide polymorphism )

Brad A. Chapman *{dagger}, John E. Bowers *, Frank A. Feltus *, and Andrew H. Paterson *{dagger}{ddagger}{sect}

*Plant Genome Mapping Laboratory and Departments of {dagger}Plant Biology, {ddagger}Genetics, and {sect}Crop and Soil Science, University of Georgia, Athens, GA 30602

Edited by Tomoko Ohta, National Institute of Genetics, Mishima, Japan, and approved December 8, 2005 (received for review September 13, 2005)

Genome duplication followed by massive gene loss has permanently shaped the genomes of many higher eukaryotes, particularly angiosperms. It has long been believed that a primary advantage of genome duplication is the opportunity for the evolution of genes with new functions by modification of duplicated genes. If so, then patterns of genetic diversity among strains within taxa might reveal footprints of selection that are consistent with this advantage. Contrary to classical predictions that duplicated genes may be relatively free to acquire unique functionality, we find among both Arabidopsis ecotypes and Oryza subspecies that SNPs encode less radical amino acid changes in genes for which there exists a duplicated copy at a "paleologous" locus than in "singleton" genes. Preferential retention of duplicated genes encoding long complex proteins and their unexpectedly slow divergence (perhaps because of homogenization) suggest that a primary advantage of retaining duplicated paleologs may be the buffering of crucial functions. Functional buffering and functional divergence may represent extremes in the spectrum of duplicated gene fates. Functional buffering may be especially important during "genomic turmoil" immediately after genome duplication but continues to act {approx}60 million years later, and its gradual deterioration may contribute cyclicality to genome duplication in some lineages.

Author contributions: B.A.C., J.E.B., and A.H.P. designed research; B.A.C., J.E.B., and F.A.F. performed research; B.A.C., J.E.B., and F.A.F. contributed new reagents/analytic tools; B.A.C., J.E.B., F.A.F., and A.H.P. analyzed data; and B.A.C., F.A.F., and A.H.P. wrote the paper.

Conflict of interest statement: No conflicts declared.

To whom correspondence should be addressed at: Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602.

Andrew H. Paterson, E-mail: paterson{at}uga.edu

www.pnas.org/cgi/doi/10.1073/pnas.0507782103
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