Abstract
Sheath blight disease is one of the predominant diseases of rice and it is caused by the necrotrophic fungal pathogen Rhizoctonia solani. The mechanistic insight about its widespread success as a broad host range pathogen is limited. In this study, we endeavor to identify pathogenicity determinants of R. solani during infection process in rice. Through RNAseq analysis, we identified a total of 65 and 232 R. solani (strain BRS1) genes to be commonly upregulated in three different rice genotypes (PB1, Tetep, and TP309) at establishment and necrotrophic phase, respectively. The induction of genes encoding extracellular protease, ABC transporter, and transcription factors were notable during establishment phase. While during necrotrophic phase, several CAZymes, sugar transporters, cellular metabolism, and protein degradation-related genes were prominently induced. We have also identified few putative secreted effector encoding genes that were upregulated during pathogenesis. The qPCR analysis further validated the phase-specific expression dynamics of some selected putative effectors and pathogenicity-associated genes. Overall, the present study reports identification of key genes and processes that might be crucial for R. solani pathogenesis. The ability to effectively damage host cell wall and survive in hostile plant environment by managing oxidative stress, cytotoxic compounds, etc. is being proposed to be important for pathogenesis of R. solani in rice. The functional characterization of these genes would provide key insights about this important pathosystem and facilitate development of strategies to control this devastating disease.
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Acknowledgements
SG is supported by SPM fellowship from Council of Scientific and Industrial Research (Govt. of India). PK is supported by Post-Doctoral Research fellowship from Department of Biotechnology (DBT, Govt. of India). We acknowledge Nucleome Informatics Pvt. Ltd for assistance in RNAseq. The assistance of central instrumentation facilities of NIPGR for qPCR is acknowledged. This work was supported by DBT, Government of India as well as core research Grant from National Institute of Plant Genome Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Communicated by M. Kupiec.
Accession Number: The Illumina sequence data from this study have been submitted as BioProject ID: PRJNA298635 to the NCBI Sequence read archive.
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Online Resource 1: Pipeline used to delineate in-planta upregulated phase-specific transcripts of R. solani during its pathogenesis in rice (TIF 113 KB)
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Online Resource 2: Heat map of differentially regulated genes of R. solani showing distinct induction patterns (TIF 1016 KB)
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Online Resource 4: R. solani transcripts expressed during infection in three different rice genotypes (PB1, Tetep and TP309) at establishment, necrotrophic and common in both the phases (XLSX 68 KB)
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Online Resource 5: GO annotation of in-planta upregulated genes of R. solani during different phases of pathogenesis (XLSX 20 KB)
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Online Resource 6: Induction pattern of R. solani transcripts encoding CAZymes during different phases of pathogenesis (XLSX 34 KB)
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Online Resource 7: R. solani genes having >2 log fold difference between susceptible (PB1 and TP309) and partially resistant (Tetep) interactions (XLSX 14 KB)
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Online Resource 8: Induction pattern of R. solani transcripts encoding sugar transporters during different phases of pathogenesis (XLSX 14 KB)
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Online Resource 9: Induction pattern of R. solani transcripts encoding putative secreted effectors during different phases of pathogenesis (XLSX 16 KB)
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Online Resource 10: Induction pattern of R. solani transcripts showing homology to PHI-base during different phases of pathogenesis. The homology of R. solani strain BRS1 genes with other R. solani strains belonging to different anastomosis groups are summarized (XLSX 31 KB)
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Online Resource 11: Correlation of qPCR and RNAseq based differential expression quantification of a few R. solani genes induced during pathogenesis on PB1 (susceptible) rice genotype (DOCX 16 KB)
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Online Resource 12: Correlation of qPCR and RNAseq based differential expression quantification of a few R. solani genes induced during pathogenesis on susceptible (PB1) and partially resistant (Tetep) rice genotype (DOCX 15 KB)
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Ghosh, S., Kanwar, P. & Jha, G. Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice. Curr Genet 64, 729–740 (2018). https://doi.org/10.1007/s00294-017-0791-7
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DOI: https://doi.org/10.1007/s00294-017-0791-7