Abstract
Magnaporthe oryzae is one of the fungal pathogens of rice which results in heavy yield losses worldwide. Understanding the genomic structure of M. oryzae is essential for appropriate deployment of the blast resistance in rice crop improvement programs. In this study we sequenced two M. oryzae isolates, RML-29 (avirulent) and RP-2421 (highly virulent) and performed comparative study along with three publically available genomes of 70-15, P131, and Y34. We identified several candidate effectors (>600) and isolate specific sequences from RML-29 and RP-2421, while a core set of 10013 single copy orthologs were found among the isolates. Pan-genome analysis showed extensive presence and absence variations (PAVs). We identified isolate-specific genes across 12 isolates using the pan-genome information. Repeat analysis was separately performed for each of the 15 isolates. This analysis revealed ∼25 times higher copy number of short interspersed nuclear elements (SINE) in virulent than avirulent isolate. We conclude that the extensive PAVs and occurrence of SINE throughout the genome could be one of the major mechanisms by which pathogenic variability is emerging in M. oryzae isolates. The knowledge gained in this comparative genome study can provide understandings about the fungal genome variations in different hosts and environmental conditions, and it will provide resources to effectively manage this important disease of rice.
Highlights
Rice is one of the most important food security crops of developing countries
Molecular understanding of repeat elements in the rice blast fungus offers an insight into their effects on genome evolution process, and sheds light on the mechanisms of pathogenic adaptation attained by different strains
In the pan-genome analysis, we found several isolate-specific genes identified from each of the 12 different Magnaporthe isolates that might be gained or lost during the course of evolution and might have roles in their pathogenicity events and their host-pathogen interactions
Summary
Rice is one of the most important food security crops of developing countries. It has been reported that more than one-third of the world’s population depend on it for their major calorific intake (Goff, 1999). The most devastating and economically significant disease that affects rice crops is a rice blast disease, produced by the fungal pathogen Magnaporthe oryzae This disease has been a major problem in the most rice-producing areas and causes substantially huge yield losses of up to 30% in all parts of the world, under favorable environmental conditions (Talbot, 2003; Skamnioti and Gurr, 2009). This disease can be effectively managed by the use of fungicides, use of Abbreviations: contig, contiguous; InDel, insertions-deletions; SINE, short interspersed nuclear element; SNP, single nucleotide polymorphism. Blast disease resistance in rice is contingent on the existence of a related cognate avirulence (Avr) gene in M. oryzae and follows a typical gene-for-gene hypothesis (Flor, 1971; Valent, 1990)
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