## 3 Results and Discussion
### Transcriptome Sequencing and Functional Annotation of Differentially Expressed Genes (DEGs)  
To understand the genome-wide transcriptional changes under different light sources in _L. edodes_, we carried out a RNA-seq analysis with different light conditions. After quality evaluation and trimming, over 2.2 million trimmed reads on average were generated from each mushroom sample in the dark (no light, NL) and blue light (BL) conditions (Table 2). Over 74% of the sequenced data (average mapping rate: 75.5%) were mapped to assemble the transcripts from the new reference genome sequence with the JGI database in this study. The duplication ratio and GC content ranged between 42.66-46.86% and 47.35-47.66%, respectively. The average 6.7 million, 1.4 million, 5.1 million, and 1.5 million reads of each sample mapped to the exonic region, intronic intergenic, and intronic/intergenic overlapping exon of the gene structure, respectively (Table 2). In addition, principal component analysis (PCA) was performed with specific features derived from alignment, including coverage, GC content, insert size, and mapping quality of each sample, and shown in Figure S2. \begin{table}
\begin{tabular}{c c c c c c} \hline \multirow{2}{*}{**Light Source**} & \multicolumn{2}{c}{**Pileus**} & \multicolumn{2}{c}{**Stipe**} & **Pileus Diameter/** \\ \cline{2-5}  & **Diameter (mm)** & **Thickness (mm)** & **Length (mm)** & **Diameter (mm)** & **Stipe Length** \\ \hline Fluorescent lamp & 53.25 \(\pm\) 2.87 b  & 19.42 \(\pm\) 1.19 cd  & 42.77 \(\pm\) 1.00 c  & 13.83 \(\pm\) 1.00 ab  & 1.25 \(\pm\) 0.07 c  \\ White LED & 55.68 \(\pm\) 2.38 ab  & 20.07 \(\pm\) 1.13 bed  & 41.28 \(\pm\) 0.44 c  & 13.45 \(\pm\) 1.06 abc  & 1.35 \(\pm\) 0.06 bc  \\ White–Green LED & 57.27 \(\pm\) 0.68 ab  & 22.63 \(\pm\) 0.44 ab  & 40.73 \(\pm\) 2.06 c  & 11.37 \(\pm\) 0.45 d  & 1.42 \(\pm\) 0.07 bc  \\ White–Blue LED & 59.38 \(\pm\) 1.95 ab  & 24.62 \(\pm\) 0.79 a  & 39.10 \(\pm\) 1.66 c  & 14.03 \(\pm\) 0.35 a  & 1.54 \(\pm\) 0.10 b  \\ Red LED & 46.17 \(\pm\) 1.68 c  & 20.85 \(\pm\) 0.20 bc  & 51.45 \(\pm\) 1.65 a  & 11.93 \(\pm\) 0.19 bcd  & 0.90 \(\pm\) 0.03 d  \\ Green LED & 54.27 \(\pm\) 1.09 ab  & 20.93 \(\pm\) 0.70 bc  & 43.63 \(\pm\) 1.59 bc  & 12.78 \(\pm\) 0.40 ab  & 1.25 \(\pm\) 0.04 c  \\ Blue LED & 60.13 \(\pm\) 0.72 a  & 22.70 \(\pm\) 0.19 ab  & 32.43 \(\pm\) 1.05 d  & 10.93 \(\pm\) 0.31 d  & 1.87 \(\pm\) 0.08 a  \\ Dark (no light) & 35.63 \(\pm\) 5.24 d  & 17.89 \(\pm\) 1.76 d  & 48.62 \(\pm\) 5.17 ab  & 11.56 \(\pm\) 0.25 cd  & 0.73 \(\pm\) 0.04 d  \\ \hline \end{tabular} Values followed by the same letter do not differ significantly at \(p>\) 0.05 according to [PERSON]’s multiple range test.  
\end{table} 
Table 1: Summary of morphological properties of the fruit body under different light sources. A total of 1,416 genes were expressed in at least one of six samples with a \(p\)-value less than 0.05. Among them, 338 and 246 genes showed a \(\log_{2}\) fold change with up and downregulation in the BL condition, respectively (Table S3). The transcriptome data reported for DEGs specific to blue light cultivation condition in our previous study [11] were different from what is reported here for GSEA analysis, transcription factors, lignocellulosic, and CAZyme for carbohydrates in mushrooms. To better understand the significant DEGs affected by the light sources, over-representation of the GO terms with the DEGs was determined by GSEA analysis (Figure 1 and Table S4). These were categorized into functional groups and displayed by an enrichment map in Cytoscape. Significant GO representations (\(p\)-value \(<\) 0.05, FDR \(<\) 0.25) were mainly related to the regulation of cell morphogenesis, such as cell shape, cytoskeleton, and DNA repair, including non-recombinational repair and double-strand repair. In addition, transcription- and translation-related genes, such as transcription factor complex, RNA polymerase activity, and translation initiation factor, were significantly expressed in different light sources.