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

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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