Table4_Transcriptome Analysis Explored the Differential Genes’ Expression During the Development of the Stropharia rugosoannulata Fruiting Body.XLSX

Stropharia rugosoannulata (S. rugosoannulata) is a fungus with great edible and nutritional values; however, the development mechanism of its fruiting body has not been studied. Thus, this study aimed to analyze the differentially expressed genes (DEGs) in four stages; primordia stage (Sra1), young mushroom stage (Sra2), picking stage (Sra3), and opening umbrella stage (Sra4). Therefore, total RNA was extracted for further RNA-sequencing analysis. In three pairwise comparison groups (PCGs), Sra1 vs. Sra2, Sra2 vs. Sra3, and Sra3 vs. Sra4, a total of 3,112 DEGs were identified among the three PCGs. A GO analysis of the DEGs showed that there were 21 terms significantly enriched in Sra1 vs. Sra2 PCG. There was no significantly enriched GO term in the other two PCGs. Furthermore, KEGG pathway analysis showed that these DEGs were mainly enriched in glucose and amino acid metabolisms. Moreover we found that intron retention (IR) and the alternative 3′ splice site (A3SS) accounted for more than 80%. The development of the S. rugosoannulata fruiting body mainly involved glucose and amino acid metabolisms. IR and A3SS were the two main types of ASE, which played an important role in the development and maturation of the S. rugosoannulata fruiting body.

大球盖菇（Stropharia rugosoannulata, S. rugosoannulata）是一种兼具极高食用与营养价值的真菌，但其子实体发育机制尚未得到深入研究。本研究旨在分析其四个发育阶段的差异表达基因（differentially expressed genes, DEGs）：原基阶段（Sra1）、幼菇阶段（Sra2）、采摘阶段（Sra3）以及开伞阶段（Sra4）。研究人员提取总RNA以开展后续的RNA测序（RNA-sequencing）分析。在三组两两比较组（pairwise comparison groups, PCGs），即Sra1 vs. Sra2、Sra2 vs. Sra3与Sra3 vs. Sra4中，共鉴定得到3112个差异表达基因。对上述差异表达基因的基因本体论（Gene Ontology, GO）分析显示，在Sra1 vs. Sra2比较组中存在21个显著富集的GO条目；其余两组则未检测到显著富集的GO条目。此外，京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路分析结果表明，这些差异表达基因主要富集于葡萄糖代谢与氨基酸代谢通路。本研究还发现，内含子保留（intron retention, IR）与可变3'剪接位点（alternative 3′ splice site, A3SS）这两类可变剪接事件（alternative splicing events, ASE）占总事件的比例超过80%。综上，大球盖菇子实体发育过程主要涉及葡萄糖与氨基酸代谢，而内含子保留与可变3'剪接位点是两种主要的可变剪接事件，在大球盖菇子实体的发育与成熟过程中发挥重要调控作用。