Extensive concerted evolution of rice paralogs and the road to regaining independence

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 similar to 0.4 MY since their divergence, with a gradual progression toward independent evolution of older paralogs. Since divergence from subspecies indica, similar to 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 similar to 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 similar to 41 WA. 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.