Whole genome comparative study of Magnaporthe oryzae field isolates reveals variation during domestication

Magnaporthe oryzae is the most destructive rice disease in world. In order to elucidate the genome variation during long term interaction with different cultivated rice strains, here we present the sequencing and comparative genomics study of two field M.o. isolates from China which contain at least 6 un-cloned Avr genes such as AvrPi-2, AvrPi-z. Compared to the reference 70-15 genome sequence and annotation, average divergence in the coding region of the two field isolates is: 1.21×10^-4 and 0.62×10^-4 respectively. The telomere region shows high density of SNPs and contains the highest density of SNPs along each chromosome. In total, it was also observed 15 genes including two secreted proteins were under positive selection, which may play a critical role in the M.o. adaptation process. Copy number Variation analysis indicated that over 158 (108 belong to M.o.-specific genes) may be duplicated during domestication; Moreover, one of the sequenced isolates from Fujian Province, China contained ~ 1.7Mb unique contigs containing over 118 novo genes and 27 out of them were considered as candidate effectors. In all, our whole genome variation study in these two field isolates provides new clues for M.o. Avr gene cloning and following association genetic study