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Genetics, Vol. 177, 1753-1763, November 2007, Copyright © 2007
doi:10.1534/genetics.107.073197

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Extensive Concerted Evolution of Rice Paralogs and the Road to Regaining Independence

Xiyin Wang, Haibao Tang, John E. Bowers, Frank A. Feltus and Andrew H. Paterson1

Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602

1 Corresponding author: Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd., Room 228, Athens, GA 30602.
E-mail: paterson{at}uga.edu

Many genes duplicated by whole-genome duplications (WGDs) are more similar to one another than expected. We investigated whether concerted evolution through conversion and crossing over, well-known to affect tandem gene clusters, also affects dispersed paralogs. Genome sequences for two Oryza subspecies reveal appreciable gene conversion in the ~0.4 MY since their divergence, with a gradual progression toward independent evolution of older paralogs. Since divergence from subspecies indica, ~8% of japonica paralogs produced 5–7 MYA on chromosomes 11 and 12 have been affected by gene conversion and several reciprocal exchanges of chromosomal segments, while ~70-MY-old "paleologs" resulting from a genome duplication (GD) show much less conversion. Sequence similarity analysis in proximal gene clusters also suggests more conversion between younger paralogs. About 8% of paleologs may have been converted since rice–sorghum divergence ~41 MYA. Domain-encoding sequences are more frequently converted than nondomain sequences, suggesting a sort of circularity—that sequences conserved by selection may be further conserved by relatively frequent conversion. The higher level of concerted evolution in the 5–7 MY-old segmental duplication may reflect the behavior of many genomes within the first few million years after duplication or polyploidization.






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Copyright © 2007 by the Genetics Society of America.