De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

Abstract

BackgroundSheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth.ResultsThe genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future.ConclusionsLarge set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2599-0) contains supplementary material, which is available to authorized users.

Secondary metabolite arsenal of an opportunistic pathogenic fungus

“…Following on trypacidin, helvolic acid also exhibits antiprotozoal activity [67] and is produced by several fungal spp. in addition to A. fumigatus, including several plant and insect pathogens and many endophytes [28,68,69]. Along with gliotoxin and fumagillin, helvolic acid exhibits cilioinhibitory activity [70] and is a potent antimicrobial [71].…”

Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

“…The groups having at least one copy of gene from each genome were considered as core orthologous groups (COGs). Based on orthoMCL clustering, protein sequences of single copy ortholog gene groups from six species were aligned and inferred phylogenetic relationship as described previously [29]. The consensus phylogenetic tree was drawn using FigTree V1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/).…”

Dissecting Parameters Associated with Sheath Rot (<i>Sarocladium oryzae</i> [(Sawada) W. Gams & D. Hawksw]) Disease in Rice (<i>Oryza sativa</i> L.

“…Pathogen produces phytotoxins, viz. cerulenin and helvoic acid [6][7][8][9] and whole genome sequencing of S. oryzae from our group revealed genes involved in production of cerulenin and helvoic acid 10 . These phytotoxins are responsible for production of greyish-brown necrotic lesion in flag leaf sheath and restricts translocation of photosynthates to the developing panicles, causing quantitative (chaffy grains) and qualitative yield loss including discolouration of grains, reduced seed viability, nutritional and market value 8,11 .…”