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Network analysis of publicly available RNA-seq provides insights into the molecular mechanisms of plant defense against multiple fungal pathogens in Arabidopsis thaliana
Cynthia Cardinault
Kevin Childs
ELSA BEATRIZ GONGORA CASTILLO
Acceso Abierto
Atribución-NoComercial-SinDerivadas
10.3390/genes14122223
PUBLIC RNA-SEQ DATASETS
WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS
GENE MODULE
ARABIDOPSIS
FUNGAL PATHOGENS
PLANT DEFENSE
Fungal pathogens can have devastating effects on global crop production, leading to annual economic losses ranging from 10% to 23%. In light of climate change-related challenges, researchers anticipate an increase in fungal infections as a result of shifting environmental conditions. However, plants have developed intricate molecular mechanisms for effective defense against fungal attacks. Understanding these mechanisms is essential to the development of new strategies for protecting crops from multiple fungi threats. Public omics databases provide valuable resources for research on plant–pathogen interactions; however, integrating data from different studies can be challenging due to experimental variation. In this study, we aimed to identify the core genes that defend against the pathogenic fungi Colletotrichum higginsianum and Botrytis cinerea in Arabidopsis thaliana. Using a custom framework to control batch effects and construct Gene Co-expression Networks in publicly available RNA-seq dataset from infected A. thaliana plants, we successfully identified a gene module that was responsive to both pathogens. We also performed gene annotation to reveal the roles of previously unknown protein-coding genes in plant defenses against fungal infections. This research demonstrates the potential of publicly available RNA-seq data for identifying the core genes involved in defending against multiple fungal pathogens.
2023
Artículo
Genes 2023, 14, 2223.https:// doi.org/10.3390/genes14122223
Inglés
Soto-Cardinault, C.; Childs, K.L.; Góngora-Castillo, E. Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana. Genes 2023, 14, 2223.https:// doi.org/10.3390/genes14122223
BIOLOGÍA MOLECULAR DE PLANTAS
Versión publicada
publishedVersion - Versión publicada
Aparece en las colecciones: Artículos de Investigación Arbitrados

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