Dataset Information

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

ABSTRACT: Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM?>?10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA). We compared the different genes assigned to each module and the biological interpretations of gene co-expression networks at early and later modules in the two rice genotypes to reveal differential responses to AG1 IA. Our results show that different changes occurred in the two rice genotypes and that the modules in the two groups contain a number of candidate genes possibly involved in pathogenesis, such as the VQ protein. Furthermore, these gene co-expression networks provide comprehensive transcriptional information regarding gene expression in rice in response to AG1 IA. The co-expression networks derived from our data offer ideas for follow-up experimentation that will help advance our understanding of the translational regulation of rice gene expression changes in response to AG1 IA.

SUBMITTER: Zhang J

PROVIDER: S-EPMC6097106 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Zhang Jinfeng J Zhao Wenjuan W Fu Rong R Fu Chenglin C Wang Lingxia L Liu Huainian H Li Shuangcheng S Deng Qiming Q Wang Shiquan S Zhu Jun J Liang Yueyang Y Li Ping P Zheng Aiping A

Functional & integrative genomics 20180505 5

Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene ...[more]

PMID: 29730773

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Project description:Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mechanism of sclerotia formation is important for crop disease control. To identify the genes involved in this process for the development of disease control targets, the transcriptomes of this species were determined at three important developmental stages (mycelium, sclerotial initiation, and sclerotial maturation) using an RNA-sequencing approach. A total of 5,016, 6,433, and 5,004 differentially expressed genes (DEGs) were identified in the sclerotial initiation vs. mycelial, sclerotial maturation vs. mycelial, and sclerotial maturation vs. sclerotial initiation stages, respectively. Moreover, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses showed that these DEGs were enriched in diverse categories, including oxidoreductase activity, carbohydrate metabolic process, and oxidation-reduction processes. A total of 12 DEGs were further verified using reverse transcription quantitative PCR. Among the genes examined, NADPH oxidase 1 (NOX1) and superoxide dismutase (SOD) were highly induced in the stages of sclerotial initiation and maturation. In addition, the highest reactive oxygen species (ROS) production levels were detected during sclerotial initiation, and enzyme activities of NOX1, SOD, and catalase (CAT) matched with the gene expression profiles. To further evaluate the role of ROS in sclerotial formation, R. solani AG1 IA was treated with the CAT inhibitor aminotriazole and H2O2, resulting in the early differentiation of sclerotia. Taken together, this study provides useful information toward understanding the molecular basis of R. solani AG1 IA sclerotial formation and maturation, and identified the important role of ROS in these processes.

Project description:Zoysia japonica brown spot was caused by necrotrophic fungus Rhizoctonia solani invasion, which led to severe financial loss in city lawn and golf ground maintenance. However, little was known about the molecular mechanism of R. solani pathogenicity in Z. japonica. In this study we examined early stage interaction between R. solani AG1 IA strain and Z. japonica cultivar "Zenith" root by cell ultra-structure analysis, pathogenesis-related proteins assay and transcriptome analysis to explore molecular clues for AG1 IA strain pathogenicity in Z. japonica. No obvious cell structure damage was found in infected roots and most pathogenesis-related protein activities showedg a downward trend especially in 36 h post inoculation, which exhibits AG1 IA strain stealthy invasion characteristic. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database classification, most DEGs in infected "Zenith" roots dynamically changed especially in three aspects, signal transduction, gene translation, and protein synthesis. Total 3422 unigenes of "Zenith" root were predicted into 14 kinds of resistance (R) gene class. Potential fungal resistance related unigenes of "Zenith" root were involved in ligin biosynthesis, phytoalexin synthesis, oxidative burst, wax biosynthesis, while two down-regulated unigenes encoding leucine-rich repeat receptor protein kinase and subtilisin-like protease might be important for host-derived signal perception to AG1 IA strain invasion. According to Pathogen Host Interaction (PHI) database annotation, 1508 unigenes of AG1 IA strain were predicted and classified into 37 known pathogen species, in addition, unigenes encoding virulence, signaling, host stress tolerance, and potential effector were also predicted. This research uncovered transcriptional profiling during the early phase interaction between R. solani AG1 IA strain and Z. japonica, and will greatly help identify key pathogenicity of AG1 IA strain.

Dataset Information

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Publications

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Similar Datasets

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