Unraveling the changes in important molecular mechanisms of Arabidopsis thaliana infected by Botrytis cinerea: insights from in silico analysis

Botrytis cinerea is one of the most important harmful fungi affecting agricultural products. This study focused on the expression changes of Arabidopsis thaliana infected with this fungus. The expression dataset of a microarray and two RNA-sequencing were integrated using the respective software. The list of differentially expressed genes was extracted, and the key genes with altered expression were identified through Cytoscape software. These key genes co-expression patterns and functional enrichment were analyzed. Subsequently, microRNAs and transcription factors associated with these genes were predicted. Ten genes, including GAPA-۲, SBPASE, CRB, HCEF۱, CaS, ATPD, LIL۳:۱, PSAH۲, PRK, and PMDH۲, were identified as crucial down-regulated genes. Additionally, ten genes, namely WRKY۳۳, CZF۱, SZF۱, STZ, ERF۱۱, RHL۴۱, BAP۱, AT۱G۰۷۱۳۵, CMPG۲, and TET۸, were highlighted as key up-regulated genes. The key roles of the hub genes with a decreased expression included processes and pathways associated with the reductive pentose phosphate cycle, photosynthesis, cold response, fructose and sucrose metabolism, defense response against bacteria, and gluconeogenesis. The key over-expressed genes played important roles in responding to chitin, oxygen deprivation, temperature fluctuations, injuries, fungal attacks, and gene transcription functions. Key genes were associated with ath-miR۸۵۰, ath-miR۳۹۳a-۵p, and ath-miR۳۹۳b-۵p. Transcription factor SPL۷ was linked to the transcription of down-regulated key genes, while transcription factors SARD۱, PIF۵, CAMTA۱, HY۵, WRKY۳۳, TOC۱, CAMTA۳, CAMTA۲, BZR۱, FAR۱, and CAMTA۵ were also predicted to be associated with up-regulated genes. Some of these results have not previously been reported. Therefore, they could be used to design practical experiments exploring the interaction between plants and pathogenic fungi.

کلیدواژه ها:

Microarray ، RNA-sequencing ، Botrytis cinerea ، Arabidopsis thaliana