Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae

Abstract

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

“…5). This result suggests that TE-driven evolution might have less of an effect on the synergistic interactions of U. virens and rice than on some other host-pathogen interactions, such as M. oryzae and rice 35,41 .…”

“…Repetitive elements often play important roles in genome evolution, including birth/death and diversification of functional genes such as effector genes, secondary metabolite biosynthesis genes 35,41 . However, no direct correlation between candidate effectors and TE-rich regions (low GC content) was evident in the U. virens genome (Fig.…”

N-Glycosylation of Effector Proteins by an α-1,3-Mannosyltransferase Is Required for the Rice Blast Fungus to Evade Host Innate Immunity

“…One was the field isolate P131 (Peng and Shishiyama, 1988;Xue et al, 2012), which was used to generate all mutant strains. The other was S1528, which was used to perform genetic crosses with P131.…”

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

“…The agent of rice blast disease, M. oryzae, is the most devastating pathogen of rice, and it can also infect other important crops, including wheat and barley. The pathogen evolves rapidly and exhibits a multitude of species-specific and cultivar-specific races (2)(3)(4)(5). Species in the M. oryzae complex have therefore become a leading model for the study of interactions between plants and their pathogens (3).…”