Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a devastating disease of rice worldwide. Among the 85 mapped resistance (R) genes against blast, 13 have been cloned and characterized. However, how these genes originated and how they evolved in the Oryza genus remains unclear. We previously cloned the rice blast R-genes Pi2, Pi9, and Piz-t, and analyzed their genomic structure and evolution in cultivated rice. In this study, we determined the genomic sequences of the Pi2/9 locus in four wild Oryza species representing three genomes (AA, BB and CC). The number of Pi2/9 family members in the four wild species ranges from two copies to 12 copies. Although these genes are conserved in structure and categorized into the same subfamily, sequence duplications and subsequent inversions or uneven crossing overs were observed, suggesting that the locus in different wild species has undergone dynamic changes. Positive selection was found in the leucine-rich repeat region of most members, especially in the largest clade where Pi9 is included. We also provide evidence that the Pi9 gene is more related to its homologues in the recurrent line and other rice cultivars than to those in its alleged donor species O. minuta, indicating a possible origin of the Pi9 gene from O. sativa. Comparative sequence analysis between the four wild Oryza species and the previously established reference sequences in cultivated rice species at the Pi2/9 locus has provided extensive and unique information on the genomic structure and evolution of a complex R-gene cluster in the Oryza genus.
稻瘟病是由真菌稻瘟病菌引發(fā)的全球破壞性水稻疾病。在已定位85個(gè)抗性基因（R）中， 13個(gè)被克隆和鑒定。然而對(duì)于這些基因的起源以及在水稻中是如何進(jìn)化的仍不明確。我們之前克隆了稻瘟病R基因Pi2、Pi9和Piz-t，并分析了它們?cè)谠耘嗟局械幕蚪Y(jié)構(gòu)和進(jìn)化。在本項(xiàng)研究中，我們確定了代表3種基因組（AA、BB和CC）的4個(gè)野生稻種中Pi2/9位點(diǎn)的基因組序列。在4個(gè)野生種中Pi2/9家族成員數(shù)量范圍從2個(gè)拷貝到12個(gè)拷貝。盡管這些基因結(jié)構(gòu)保守并且屬于同一個(gè)亞家族，但是出現(xiàn)的序列重復(fù)和反轉(zhuǎn)或不均勻的跨越表明不同的野生種中該基因位點(diǎn)已發(fā)生了動(dòng)態(tài)變化。大多數(shù)成員的富含亮氨酸重復(fù)區(qū)域存在正向選擇，特別是在包含了Pi9的最大分支上。我們還證明在回歸系及其他水稻品種中Pi9與其同系物的相關(guān)性要比其供體物種小粒野生稻中同系物的親緣性更近，這表明Pi9可能起源自栽培稻。通過(guò)比對(duì)分析Pi2/9基因座在四個(gè)野生稻品種和先前多個(gè)栽培稻品種中的序列，為研究稻瘟病抗性基因簇的基因結(jié)構(gòu)和進(jìn)化提供了廣泛獨(dú)特的信息。