## 3 Results and Discussion
### Transcriptome Sequencing and Functional Annotation of Differentially Expressed Genes (DEGs)
\begin{table}
\begin{tabular}{c c c c c c c c c} \hline \hline \multirow{2}{*}{**Sample**} & \multirow{2}{*}{\begin{tabular}{c} **Total** \\ **Reads** \\ **/Rate (\%)** \\ \end{tabular} } & \multirow{2}{*}{\begin{tabular}{c} **Mapped** \\ **Reads** \\ **/Rate (\%)** \\ \end{tabular} } & \multirow{2}{*}{\begin{tabular}{c} **Duplication** \\ **Rate (\%)** \\ \end{tabular} } & \multirow{2}{*}{\begin{tabular}{c} **GC** \\ **Content (\%)** \\ \end{tabular} } & \multirow{2}{*}{**Exonic**} & \multirow{2}{*}{**Intronic**} & \multirow{2}{*}{\begin{tabular}{c} **Intronic/** \\ **Intergenic** \\ **Overlapping** \\ **Exon:** \\ \end{tabular} } \\ \hline blue light\_1 & 21,176,451 & \begin{tabular}{c} 15,896,792 \\ /75.1 \\ \end{tabular} & 44.19 & 47.45 & 6,371,649 & 1,323,094 & 4,725,629 & 1,453,657 \\ \hline blue light\_2 & 21,053,355 & \begin{tabular}{c} 16,067,707 \\ /76.3 \\ \end{tabular} & 46.86 & 47.57 & 6,681,571 & 1,380,842 & 4,680,733 & 1,516,080 \\ \hline blue light\_3 & 17,564,307 & \begin{tabular}{c} 13,356,006 \\ /76.0 \\ \end{tabular} & 42.66 & 47.52 & 5,656,474 & 1,149,817 & 3,785,002 & 1,271,736 \\ \hline no light\_1 & 23,688,201 & \begin{tabular}{c} 17,545,089 \\ /74.1 \\ \end{tabular} & 43.91 & 47.31 & 6,285,984 & 1,276,813 & 5,857,490 & 1,413,930 \\ \hline no light\_2 & 25,593,815 & \begin{tabular}{c} 19,262,298 \\ /75.3 \\ \end{tabular} & 46.86 & 47.4 & 7,417,614 & 1,544,413 & 6,028,425 & 1,704,375 \\ \hline no light\_3 & 23,973,170 & \
\begin{tabular}{c} 18,274,632 \\ /76.2 \\ \end{tabular} & 45 & 47.51 & 7,649,221 & 1,525,141 & 5,298,595 & 1,694,124 \\ \hline Average & 22,174,883 &
\begin{tabular}{c} 16,733,754 \\ /75.5 \\ \end{tabular} & 44.91 & 47.46 & 6,677,086 & 1,366,687 & 5,062,646 & 1,508,984 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Summary of sequencing and mapping results. Figure 1: Gene set enrichment analysis (GSEA) of differentially expressed genes. Cytoscape and an enrichment map were used for visualization of the GSEA results. Investigation of the KOG functional categories was performed for the genes upregulated under the BL condition (Figure 2). Most of the terms were upregulated in the BL condition; among them, \"transcription,\" \"posttranslational modification,\" \"protein turnover,\" \"chaperones,\" \"signal transduction mechanisms,\" \"RNA processing and modification,\" and \"replication, recombination and repair\" had higher correlations with upregulation in the BL condition than in the NL condition. These results correspond with the GSEA assay and imply that light plays a significant role in the basic development and division of _L. edodes_ cells. To further evaluate the functional pathway derived by the BL condition, KEGG sub-classification was performed with the up and downregulated genes in different light sources. Coincident with the results of the GSEA and KOG analysis, \"chromosome and associated proteins,\" \"mitochondrial biogenesis,\" \"ribosome biogenesis,\" \"transcription machinery,\" and \"DNA repair and recombination proteins\" showed high matches with the upregulated genes in the BL condition (Figure 3). Figure 3: Categories classified by Kyoto Encyclopedia of Genes and Genomes (KEGG) of differentially expressed genes (DEGs, absolute fold change value set to \(\geq\)2 and \(p\) < 0.05) under blue light. Pathways are shown according to the number of DEGs. Figure 2: EuKaryotic Orthologous Groups (KOG) function classifications of differentially expressed genes (DEGs, absolute fold change value set to \(\geq\)2 and \(p\) < 0.05) under blue light. Functional predictions of DEGs were classified into 25 functional classes by the KOG database, and the functional classes are shown according to the number of DEGs. Light is a key environmental factor that influences fruiting body development in many basidiomycetes. For several decades, it has been shown that fruiting body growth, development, and differentiation in basidiomycetes are regulated by blue light [23; 24; 25; 26].