Transcriptome Analysis and Its Application in Screening Genes Related to the Growth and Development of Sarcomyxa edulis

<i>Sarcomyxa edulis</i> is a characteristic edible and medicinal mushroom found in Northeast China that is highly valued by consumers for its tender texture, pleasant flavor, and high nutritional value. To gain a deeper understanding of the molecular mechanisms underlying the development of <i>S. edulis</i> fruiting bodies, this study utilized the Illumina NovaSeq platform to perform transcriptome sequencing at three growth and development stages of <i>S. edulis</i> strain SE8, namely primordia (SE8-P), fruiting body differentiation (SE8-F), and mature fruiting body (SE8-M). A total of 54.67 Gb of clean data was obtained, with a GC content of around 51%. After assembly, 36,423 Unigenes were obtained. Functional annotation was performed on the Unigenes, resulting in 21,206 Unigene annotation results. Differential expression gene analysis showed that 79,606 and 523 DEGs were annotated in at least one database during the SE8-P vs. SE8-F, SE8-F vs. SE8-M, and SE8-P vs. SE8-M processes, respectively. Among these, the genes encoding aldehyde dehydrogenase and fungal hydrophobins were consistently downregulated, playing a negative regulatory role in the growth and development of <i>S. edulis</i>. The genes encoding glycoside hydrolase and AB hydrolase superfamily proteins were consistently upregulated, playing a positive regulatory role in growth and development. Among these, the genes encoding aldehyde dehydrogenase were annotated to the Tryptophan metabolism (ko00380) pathway through KEGG, suggesting that aldehyde dehydrogenase regulates indoacetate formation in the fruiting body of <i>S. edulis</i>. The accuracy of RNA-Seq and DEG analysis was validated using quantitative PCR. This study enriches our knowledge of the genetic information and provides a theoretical basis for the molecular mechanisms of fruiting body development of <i>S. edulis</i>.