| Summary: | <p>Abstract</p> <p>Background</p> <p>The <it>Pi2/9</it> locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR) genes in the rice genome. Although three functional <it>R</it>-genes have been cloned from this locus, little is known about the origin and evolutionary history of these genes. Herein, an extensive genome-wide survey of <it>Pi2/9</it> homologs in rice, sorghum, <it>Brachypodium</it> and <it>Arabidopsis</it>, was conducted to explore this theme.</p> <p>Results</p> <p>In our study, 1, 1, 5 and 156 <it>Pi2/9</it> homologs were detected in <it>Arabidopsis</it>, <it>Brachypodium</it>, sorghum and rice genomes, respectively. Two distinct evolutionary patterns of <it>Pi2/9</it> homologs, Type I and Type II, were observed in rice lines. Type I <it>Pi2/9</it> homologs showed evidence of rapid gene diversification, including substantial copy number variations, obscured orthologous relationships, high levels of nucleotide diversity or/and divergence, frequent sequence exchanges and strong positive selection, whereas Type II <it>Pi2/9</it> homologs exhibited a fairly slow evolutionary rate. Interestingly, the three cloned <it>R</it>-genes from the <it>Pi2/9</it> locus all belonged to the Type I genes.</p> <p>Conclusions</p> <p>Our data show that the <it>Pi2/9</it> locus had an ancient origin predating the common ancestor of gramineous species. The existence of two types of <it>Pi2/9</it> homologs suggest that diversifying evolution should be an important strategy of rice to cope with different types of pathogens. The relationship of cloned <it>Pi2/9</it> genes and Type I genes also suggests that rapid gene diversification might facilitate rice to adapt quickly to the changing spectrum of the fungal pathogen <it>M. grisea</it>. Based on these criteria, other potential candidate genes that might confer novel resistance specificities to rice blast could be predicted.</p>
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