Genome and Transcriptome Analyses of Indian Isolates of Rice Blast Fungus, Magnaporthe oryzae

Indian subcontinent is the center of origin and diversity for Rice (Oryza sativa L.). The O. sativa ssp. indica is the major rice grown in Indian suncontinent. Rice blast disease caused by Magnaporthe oryzae is the major constraint in rice production in India. Genomes of several strains of M. oryzae have been reported ealier. However, genomic landscape of Indian strains of M. oryzae are not reported so far. Here we report the whole genome sequencing of two Magnaporthe isolates B157 and MG01 from India using next generation sequencing technology. The de novo assembly and annotation revealed 40 Mb genome with 11340 genes in B157 and 43 Mb genome with 11733 genes in MG01. Using 70-15 strain as a reference genome, we identified 11736 SNPs and 6260 short Indels in the B157 genome and 14117 SNPs and 5695 InDels in the MG01 genome. Around 75% and 70% of the annotated genes from B157 and MG01, respectively, have found to have expression evidence from RNA seq analysis. The strand specific RNA (ssRNA) seq analysis from mycelial stage of MG01  strain revealed that 7404 genes are expressed only sense transcripts and 338 genes expressed only antisense transcripts. Nearly 5% of genes (596) have expressed with  overlapping sense and antisense transcripts in MG01. The current ssRNA seq and previous digital transcriptome (MPSS and RL-SAGE) studies have supported 75 genes with overlapping sense and antisense transcript expression at the mycelial stage of Magnaporthe. This suggests that ssRNA seq is a powerful expression tool for deciphering sense and antisense nature of transcripts for genome annotated and novel genes discovery.