Abstract
BackgroundThe Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR) genes in the rice genome. Although three functional R-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 Pi2/9 homologs in rice, sorghum, Brachypodium and Arabidopsis, was conducted to explore this theme.ResultsIn our study, 1, 1, 5 and 156 Pi2/9 homologs were detected in Arabidopsis, Brachypodium, sorghum and rice genomes, respectively. Two distinct evolutionary patterns of Pi2/9 homologs, Type I and Type II, were observed in rice lines. Type I Pi2/9 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 Pi2/9 homologs exhibited a fairly slow evolutionary rate. Interestingly, the three cloned R-genes from the Pi2/9 locus all belonged to the Type I genes.ConclusionsOur data show that the Pi2/9 locus had an ancient origin predating the common ancestor of gramineous species. The existence of two types of Pi2/9 homologs suggest that diversifying evolution should be an important strategy of rice to cope with different types of pathogens. The relationship of cloned Pi2/9 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 M. grisea. Based on these criteria, other potential candidate genes that might confer novel resistance specificities to rice blast could be predicted.
Highlights
The Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR) genes in the rice genome
Identification and phylogenetic analyses of Pi2/9 homologs In order to study their evolutionary history, Pi2/9 homologs were identified in 14 rice cultivars, 12 wild rice lines, and a single accession each of sorghum, Brachypodium and A. thaliana
This locus could not be entirely reconstructed in the other 12 rice lines due to the partially sequenced fragments in this region only based on PCR productions or bacterial artificial chromosome (BAC)-end sequences (Table 1; four rice varieties used for amplification with specific primers and eight wild rice lines from BAC end sequences libraries)
Summary
The Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR) genes in the rice genome. Plants use pattern-recognition receptors (PRRs) to recognize conserved pathogen-associated molecular patterns (PAMPs) which leads to a PAMP-triggered immunity (PTI)[2]. This innate immune system can be overcome by specialized microbial pathogens by secreting some small molecules (known as effectors). Some NBS-LRR gene homologs locating at the same locus exhibited a different evolutionary pattern [13,14]. Type I genes consist of a large variety of RGC2 homologs through mass sequence exchange events, and are generally diverse with no obvious allelic/orthologous relationships in different genotypes or their close relatives. Type II homologs of RGC2 evolve slowly and are highly conserved among accessions with rare sequence exchanges [14]
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