Pattern of LRR nucleotide variation in plant resistance genes

LRR domain of plant R genes, consisting of individual LRRs with a parallel β-sheets (xxLxLxx) structure each, plays a major role in recognition specificity for pathogen effector molecules. However, little is known about variation pattern of individual LRRs. Here, we investigated nucleotide diversity, synonymous and nonsynonymous substitution for each of the LRRs in 12 functional R genes. We found that the level of nucleotide diversity and the ratio of Ka to Ks were significantly different among individual LRR units. A significant Ka > Ks was detected in 50.2% individual LRR units, ∼70% xxLxLxx motifs and ∼43% C-terminal flanking of the xxLxLxx motif, respectively, suggesting a role in these units or motifs in recognition specificity. Contrastingly, the sequences N-terminal to the xxLxLxx motif showed a very conservative evolution, similar to the non-LRR or NBS domain. Moreover, most of the xxLxLxx motifs with significant Ka > Ks values were linked, mainly locating in the C-terminal half of the LRR repeats in most of the NBS-LRR genes, which was consistent with that of the region of the recognition specificity. Uneven distribution of the LRR units with significant Ka > Ks values indicates that only some linked LRRs account for plant recognition specificity, and that diversifying selection have acted on them for profiling their functions.