Genetic signatures of plant resistance genes with known function within and between species

Plant disease resistance (R) genes have undergone significant evolutionary divergence to cope with rapid changes in pathogens. These highly variable evolutionary patterns may have contributed to diversity in R gene protein families or structures. Here, the evolutionary patterns of 76 identified R genes and their homologs were investigated within and between plant species. Results demonstrated that nucleotide binding sites and leucine-rich-repeat genes located in loci with complex evolutionary histories tended to evolve rapidly, have high variation in copy numbers, exhibit high levels of nucleotide variation and frequent gene conversion events, and also exhibit high non-synonymous to synonymous substitution ratios in LRR regions. However, non-NBS-LRR R genes are relatively well conserved with constrained variation and are more likely to participate in the basic defense system of hosts. In addition, both conserved and highly divergent evolutionary patterns were observed for the same R genes and were consistent with inter- and intra-specific distributions of some R genes. These results thus indicate either continuous or altered evolutionary patterns between and within species. The present investigation is the first attempt to investigate evolutionary patterns among all clearly functional R genes. The results reported here thus provide a foundation for future plant disease studies.