Transcriptome Analysis and SNP Identification Reveal That Heterologous Overexpression of Two Uncharacterized Genes Enhances the Tolerance of Magnaporthe oryzae to Manganese Toxicity

Wang, Yi; Liu, Lina; Pu, Xin; Ma, Chan; Qu, Hao; Wei, Mian; Zhang, Ke; Wu, Qi; Li, Chengyun

doi:10.1128/spectrum.02605-21

Cited by 3 publications

(3 citation statements)

References 79 publications

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“…Weighted correlation network analysis (WGCNA) was conducted similarly to previous protocols applied in M. oryzae. 25 The soft threshold power was 16, with R 2 > 0.8 and mean connectivity <100 according to scale-free topology criteria. The visualization of the interaction network was performed with Gephi 0.9.7.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Multiomics Analyses Reveal the Complexity of Interaction between Two Strains of Magnaporthe oryzae

Wang

et al. 2023

J. Agric. Food Chem.

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Plants growing in open environments are frequently coinfected by multiple strains of the same pathogen. However, few investigations have been carried out to reveal the outcomes and underlying mechanisms of such infections. This study aimed to observe the behaviors of two different strains under coinfection and cocultivation. We constructed an experimental system to study such interactions directly by labeling Magnaporthe oryzae strains with the green fluorescent proteins and mushroom cherry fluorescent protein to observe mixed strain behavior in vivo and in vitro. Moreover, multiomics analyses were conducted to explore the underlying mechanisms at the genomic, transcriptomic, and metabolomic levels. Our results revealed that coinfection with two strains can affect disease severity and that the more weakly virulent strain benefits from the coinfection system. We also found that amino acid variation might negatively influence such interactions at transcriptomic and metabolomic levels. In addition, we showed that the overexpression of a glutamine-related gene improved strain competitiveness during mixture cultivation. Collectively, our results provided experimental methods to analyze the interaction between two strains of M. oryzae and preliminarily explored the interacted mechanism of two strains under cocultivation through multiomics analyses.

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Section: ■ Materials and Methodsmentioning

confidence: 99%

Multiomics Analyses Reveal the Complexity of Interaction between Two Strains of Magnaporthe oryzae

Wang

et al. 2023

J. Agric. Food Chem.

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“…Supplementary Table 7 summarizes the data sets used in this study [5,41,[87][88][89][90][91]. All the analysis scripts are offered in the Additional file 3, Additional file 4 and Additional file 5.…”

Section: Data Sets and Codementioning

confidence: 99%

A comprehensive workflow for optimizing RNA-seq data analysis

Jiang,

Zheng,

Ren

et al. 2024

BMC Genomics

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Background Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge. Results By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz. Conclusion The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.

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“…The sample preparation for RNA sequencing is referenced by the previous paper [27,28]. The mycelia of Guy11 were cultivated into liquid CM for 2 days and transferred into fresh liquid CM, adding 10 µg/mL 9-phenanthrol for 24 h for RNA extraction.…”

Section: Rna Sequencingmentioning

confidence: 99%

Transcriptome and Quasi-Targeted Metabolome Analyze Overexpression of 4-Hydroxyphenylpyruvate Dioxygenase Alleviates Fungal Toxicity of 9-Phenanthrol in Magnaporthe oryzae

Wang

Jibril

et al. 2022

IJMS

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Magnaporthe oryzae, the causal agent of rice blast disease, produces devastating damage to global rice production. It is urgent to explore novel strategies to overcome the losses caused by this disease. 9-phenanthrol is often used as a transient receptor potential melastatin 4 (TRPM4) channel inhibitor for animals, but we found its fungal toxicity to M. oryzae. Thus, we explored the antimicrobial mechanism through transcriptome and metabolome analyses. Moreover, we found that overexpression of a gene encoding 4-hydroxyphenylpyruvate dioxygenase involved in the tyrosine degradative pathway enhanced the tolerance of 9-phenanthrol in M. oryzae. Thus, our results highlight the potential fungal toxicity mechanism of 9-phenanthrol at metabolic and transcriptomic levels and identify a gene involving 9-phenanthrol alleviation. Importantly, our results demonstrate the novel mechanism of 9-phenanthrol on fungal toxicity that will provide new insights of 9-phenanthrol for application on other organisms.

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Transcriptome Analysis and SNP Identification Reveal That Heterologous Overexpression of Two Uncharacterized Genes Enhances the Tolerance of Magnaporthe oryzae to Manganese Toxicity

Cited by 3 publications

References 79 publications

Multiomics Analyses Reveal the Complexity of Interaction between Two Strains of Magnaporthe oryzae

Multiomics Analyses Reveal the Complexity of Interaction between Two Strains of Magnaporthe oryzae

A comprehensive workflow for optimizing RNA-seq data analysis

Transcriptome and Quasi-Targeted Metabolome Analyze Overexpression of 4-Hydroxyphenylpyruvate Dioxygenase Alleviates Fungal Toxicity of 9-Phenanthrol in Magnaporthe oryzae

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