Transcriptome Dynamics of the Freshwater Fungus Penicillium adametzioides FBCC-F1417 Across Growth Stages

Penicillium adametzioides is a filamentous fungus commonly isolated from aquatic environments and is known to produce diverse secondary metabolites and enzymes with potential ecological significance. However, the molecular mechanisms underlying its physiological changes during growth remain largely unexplored. In this study, transcriptome sequencing was performed to investigate gene expression dynamics in the freshwater fungal strain P. adametzioides FBCC-F1417 across different growth stages. Total RNA was extracted from mycelial samples collected at four time points (0, 1, 2, and 3 days), generating 11 RNA-seq libraries that were sequenced using an Illumina paired-end platform. Raw reads were quality-filtered using Trimmomatic, producing approximately 45 million clean reads per sample with Q30 values exceeding 93%. The filtered reads were aligned to the reference genome using HISAT2, resulting in mapping ratios ranging from approximately 51% to 66%. Transcript assembly and expression quantification were conducted using StringTie, and gene expression levels were normalized as FPKM and TPM values. A total of 13,643 genes were initially detected, of which 11,557 genes passed quality filtering and were used for downstream analyses. Differential expression analysis was performed using the edgeR package with a threshold of |fold change| ≥ 2 and raw p-value < 0.05. Overall, 5,520 genes were identified as differentially expressed across the tested conditions. Hierarchical clustering and multidimensional scaling analyses revealed distinct transcriptional patterns among the growth stages. These results provide a comprehensive overview of transcriptional changes during the growth of P. adametzioides FBCC-F1417 and offer a valuable resource for understanding gene regulation, and potential secondary metabolite biosynthesis in freshwater-derived fungi.