De novo Whole Genome Assembly and Annotation of Sarocladium oryzae causing Sheath Rot Disease in Rice (Oryza sativa L.)

Sheath rot disease of rice caused by Sarocladium oryzae [(Sawada) W. Gams & D. Hawksw] belongs to Ascomycotina class of fungus and is emerging as a major disease in most of rice growing ecosystems in world.  Reports on pathogen diversity studies are very meagre and limited to toxins characterizations.  Genomic resources of S. oryzae are poorly developed and available genomic resources in public data bases are related to internal transcriber spacer (ITS) and ribosomal genes (rRNA gene).  Therefore, whole genome de nova sequencing of highly virulent strain of S. oryzae sampled from 25 different rice growing regions in South India was undertaken using Illumina Nextseq Paired-End sequencing platform with 250X genome coverage.  High quality reads were assembled into 5934 contigs/scaffolds and the genome size was found to be 32.85 Mb with N₅₀ value of 18.04 Kb.  Functional annotation of genome revealed that the fungus codes for 10526 proteins. The gene ontology studies showed 12.21, 39.1 and 47.33 per cent of genes involved in biological process, cellular and molecular functions, respectively. We have predicted 10650 simple sequences repeats which comprises of mono, di, tri, tetra, penta and hexa repeats/motifs. Genome is enriched with A/T types of mononucleotide repeats and AG/TC types of dinucleotides repeats.  The whole genome sequence will give insight into pathogenicity genes harboured in the genome of S. oryzae.  Development of SSR markers helpful for the pathogen diversity studies and fingerprinting of isolates.