Transcriptomic Profiling of mRNA and lncRNA During the Developmental Transition from Spores to Mycelia in Penicillium digitatum

The fungus <i>Penicillium digitatum</i> causes citrus green mold, a major postharvest disease. Understanding the molecular mechanisms underlying its development is crucial for devising effective control strategies. In this study, we performed a comprehensive transcriptomic analysis of <i>P. digitatum</i> across three key developmental stages: spores, germinated spores, and mycelia. A total of 2175 novel mRNAs, 3957 novel long non-coding RNAs (lncRNAs), and 144 circular RNAs (circRNAs) were identified in <i>P. digitatum</i>. Genetic variation analysis revealed 12,396 Insertion-Ddeletion and 23,264 single nucleotide polymorphisms, with their prevalence decreasing as development progressed. The expression levels, temporal expression patterns and significant differences in mRNAs and lncRNAs across different developmental stages were also observed. Functional enrichment analysis of differentially expressed mRNAs and differentially expressed lncRNA target genes highlighted key biological processes and pathways associated with macromolecular metabolism, signal transduction, DNA replication, and reactive oxygen species scavenging. Additionally, differential expression analysis explored the potential interactions between differentially expressed lncRNAs and their target genes, as well as those between lncRNAs and circRNAs. Our findings provide valuable insights into the complex regulatory networks underpinning the development and pathogenicity of <i>P. digitatum</i>, offering a foundation for future research aimed at controlling green mold.