## 2 Results
### Transcriptomic Data Evaluation  
RNA-seq analysis of 45 samples collected over the course of eight days under the two culture conditions of _P. daleae_ strain NBP-49626 generated 141,631,730,858 bp (141.6 Gb) sequence data, consisting of 944,674,938 filtered reads. The mean quality of high-quality sequences (Fastq QC > 30) following adapter trimming was 92.3 \(\pm\) 0.3%. Approximately 96.59 \(\pm\) 0.01% of the clean reads were mapped to the _P. daleae_ strain NBP-49626 genome, indicating that the quality of transcriptome sequencing data was reliable (Table S2). The transcriptome profiles exhibited significant changes at different time intervals throughout the submerged and semi-solid fermentations. A total of 2530 DEGs (fold change \(\geq\) 2.0, \(p\)-value \(\leq\) 0.05) were identified at the second day of submerged fermentation in comparison to the transcriptome level on the first day, with the number of DEGs essentially stabilizing at high levels from the fifth day onwards (5017 DEGs, Figure 4a, Tables S3 and S4); in contrast, the number of DEGs eventually stabilized at high levels during semi-solid fermentation beginning on days two and three (3042 and 4117 DEGs, respectively; Figure 4b, Tables S3 and S4). The temporal patterns in the varying levels of gene transcription were generally consistent with the trends in Okaramine B yield observed during the corresponding fermentations described above (Figure 2). Figure 3: COG function classification of the _Penicillium daleae_ NBP-49626 genome. The number on the top of the categories represents the number of genes. GO term analysis was conducted to identify the biological processes, molecular functions, and cellular components that contribute to Okaramine B production. It revealed that during the submerged fermentation process, the DEGs were primarily associated with molecular functions including oxidoreductase activity (e.g., 185 genes on day three and 275 genes on day four) and transmembrane transporter activity on the third day (117 genes), biological processes including translation (e.g., 67 genes on day three and 77 genes on day four) and carbohydrate metabolic processes between the fourth and sixth days (157, 154, and 152 genes, respectively), and cellular component terms such as membrane between the second and third days (129 and 153 genes, respectively), ribosome (e.g., 63 genes on day three and 72 genes on day four), and intracellular (e.g., 50 genes on day three and 64 genes on day four) (Figures 5a-c and S3). During the semi-solid fermentation process, the DEGs were associated with molecular functions including oxidoreductase activity and transmembrane transporter activity virtually at all times (e.g., 203 genes and 244 genes on day two, respectively), biological processes including translation (e.g., 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 17  
70 genes on day two), and especially the carbohydrate metabolic processes started on day four (135 genes), as well as cellular component terms including membrane (e.g., 143 genes on day two), ribosome (e.g., 67 genes on day two), and intracellular (e.g., 48 genes on day two). Notably, in semi-solid fermentation, DEGs involved in oxidoreductase activity and transmembrane transporter activity remained for a longer amount of time than those in submerged fermentation (Figures 5d-f and S3). KEGG analyses further revealed these DEGs to be enriched in the biosynthesis of secondary metabolites (map01110, e.g., 148 genes on day three), microbial metabolism in diverse environments (map01120, e.g., 108 genes on day three), and the biosynthesis of amino acids (map01230, e.g., 80 genes on day four) and ribosomes (map03010, e.g., 75 genes on day four) during the submerged fermentation process (Figures 6a-c and S4). On the other hand, these DEGs were mainly enriched in microbial metabolism in diverse environments (e.g., 84, 121, and 123 genes on days two, four, and six, respectively) during the semi-solid fermentation process (Figures 6d-f and S4).