DOI: 10.5061/dryad.674p4
title: Data from: De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

description: Background: Sheath 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. Results: The 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. Conclusions: Large 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.
description: WAG model of ML
 treeBased on orthoMCL
 clustering, 100 single copy ortholog gene groups from five fungal species
 were selected randomly and aligned separately using MUSCLE version 3.8.31
 with default parameters. All hundred Multiple Sequence Alignments (MSA)
 were concatenated. Then, 1000 bootstrap replicates were performed using
 SEQBOOT program in Phylip package version 3.696. The maximum-likelihood
 tree was constructed by PhyML V3.1 (--datatype aa --model WAG --bootstrap
 1000) with 1000 bootstrap replicates to infer phylogenetic relationship of
 Sarocladium oryzae in relation to other Ascomycetes fungi (Magnaporthe
 oryzae, Fusarium graminearum, Acremonium chrysogenum, and Fusarium
 oxysporum). The consensus tree constructed using CONSENSE in Phylip
 package.WAG_model_phylogeny