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Abstract
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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-2, SBPASE, CRB, HCEF1, CaS, ATPD, LIL3:1, PSAH2, PRK, and PMDH2,
were identified as crucial down-regulated genes. Additionally, ten genes, namely
WRKY33, CZF1, SZF1, STZ, ERF11, RHL41, BAP1, AT1G07135, CMPG2, and
TET8, 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 overexpressed 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-miR850, ath-miR393a-5p, and ath-miR393b-5p.
Transcription factor SPL7 was linked to the transcription of down-regulated key genes,
while transcription factors SARD1, PIF5, CAMTA1, HY5, WRKY33, TOC1,
CAMTA3, CAMTA2, BZR1, FAR1, and CAMTA5 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
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