Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin Province 130118, China; Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, Shanxi Province 044000, China.
Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin Province 130118, China.
Gene. 2022 May 25;824:146450. doi: 10.1016/j.gene.2022.146450. Epub 2022 Mar 23.
Sarcomyxa edulis is a widely harvested mushroom of Northeastern Asia. Its development can be divided into six stages: growth of mycelium until occupying half the bag (B1), mycelium under low-temperature stimulation after occupying the entire bag (B2), appearance of mycelium in primordia (B3), primordia (B4), mycelium at the harvest stage (B5), and mature fruiting body (B6). Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening key genes. To explore the growth and development mechanisms of the mushroom S. edulis and clarify its genetic background, DEG and WGCNA analyses were combined to screen key genes at different developmental stages. From A1 to A6, respectively, 459, 97, 885, 169, 277, and 712 key genes were identified. Then the Gene Ontology (GO) terms and KEGG pathways of key genes were analyzed, and GO and KEGG analyses were performed on all genes across different periods using GSEA. In summary, the genes in A1 were mainly involved in amino sugar and nucleotide sugar metabolism, structural molecule activity, and oxidative phosphorylation. At the A2 stage, genes were mainly involved in peptidase activity, peroxidase activity, oxidoreductase activity, antioxidant activity, biosynthesis of secondary metabolites, and glycolysis and gluconeogenesis. A3 genes were involved in gene expression, RNA metabolism, spliceosome, RNA transport, and ribosome biogenesis. A4 genes were mainly involved in the biosynthesis of secondary metabolites, proteasome complex, cellular protein complex assembly, actin filament-based processes, oxidative phosphorylation, and carbon metabolism. The A5 stage genes were involved in the carbohydrate metabolic process, polysaccharide metabolic process, and the biosynthesis of secondary metabolites, leucine, isoleucine, and ABC transporters. Finally, A6 genes were mainly involved in the cell cycle, meiosis of yeast, MAPK signaling pathway, cellular response to DNA damage stimulus, DNA metabolic process, DNA replication, and DNA repair. The combination of multiple analyses provides us with an in-depth understanding of the network that regulates mushroom development.
美味牛肝菌是一种广泛生长于东北亚地区的蘑菇。它的发育可以分为六个阶段：菌丝体生长至占据袋子的一半（B1），菌丝体在低温刺激下占据整个袋子（B2），菌丝体出现原基（B3），原基（B4），收获阶段的菌丝体（B5）和成熟的子实体（B6）。差异表达基因（DEG）分析和加权基因共表达网络分析（WGCNA）是筛选关键基因的重要生物信息学方法。为了探索蘑菇 S. edulis 的生长发育机制并阐明其遗传背景，将 DEG 和 WGCNA 分析相结合，以筛选不同发育阶段的关键基因。从 A1 到 A6，分别鉴定出 459、97、885、169、277 和 712 个关键基因。然后对关键基因的基因本体（GO）术语和 KEGG 途径进行了分析，并使用 GSEA 对不同时期的所有基因进行了 GO 和 KEGG 分析。总之，A1 中的基因主要参与氨基糖和核苷酸糖代谢、结构分子活性和氧化磷酸化。在 A2 阶段，基因主要参与肽酶活性、过氧化物酶活性、氧化还原酶活性、抗氧化活性、次生代谢物合成以及糖酵解和糖异生。A3 基因参与基因表达、RNA 代谢、剪接体、RNA 转运和核糖体生物发生。A4 基因主要参与次生代谢物合成、蛋白酶体复合物、细胞蛋白复合物组装、肌动蛋白丝基过程、氧化磷酸化和碳代谢。A5 阶段的基因参与碳水化合物代谢过程、多糖代谢过程以及次生代谢物、亮氨酸、异亮氨酸和 ABC 转运体的合成。最后，A6 基因主要参与细胞周期、酵母减数分裂、MAPK 信号通路、细胞对 DNA 损伤刺激的反应、DNA 代谢过程、DNA 复制和 DNA 修复。多种分析的结合使我们深入了解了调控蘑菇发育的网络。
