Using network extracted ontologies to identify novel genes with roles in appressorium development in the rice blast fungus magnaporthe oryzae
Open accessAbstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.
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Another study generated a multiscale hierarchical map from a co-expression network of a pathogenic fungus; this map was used to identify clusters in the hierarchy associated with plant cell infection, determining genes not previously reported to function in these pathways.
“Another study generated a multiscale hierarchical map from a co-expression network of a pathogenic fungus; this map was used to identify clusters in the hierarchy associated with plant cell infection, determining genes not previously reported to function in these pathways (Ames, 2017).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Ames, 2017
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- Authors
- Ames, R.
- Affiliations
- University of Exeter (GB)
- Corresponding author
- Ames, Ryan
- ORCID
- Ames, Ryan
- Venue
- Microorganisms
- Publisher
- MDPI AG
- Published
- 2017-01-17
- Volume
- 5
- Issue
- 1
- Pages
- 3
- ISSN
- 2076-2607 (ISSN-L)
- PMC
- PMC5374380
- OpenAlex
- W2574522793
- Cited by
- 10
- References
- 58
- Citations by year
- 2021: 3 · 2020: 1 · 2019: 1 · 2018: 4 · 2017: 1
- FWCI
- 0.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Microorganisms (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion)
- Open Research Exeter (University of Exeter) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (WT105618MA)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Disease Resistance and Genetics
- Keywords
- Magnaporthe oryzae, rice blast, appressorium formation, gene function prediction, novel genes, plant pathogenic fungi, RNA-seq
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