Integrated genomic and transcriptomic analysis of genes involved in fruiting body development of Panellus edulis

Introduction Panellus edulis is an edible and medicinal basidiomycete widely distributed in Northeast China and highly valued for its culinary quality and bioactive properties. To better understand the molecular mechanisms underlying fruiting body development in P. edulis , we performed whole genome and transcriptome sequencing. Methods We generated a high-quality reference genome for the monokaryotic strain SE6 -23 by integrating Illumina NovaSeq short-read sequencing with PacBio Revio long-read sequencing. Using this reference genome, we performed stage -specific RNA -seq of the SE6 strain on the Illumina NovaSeq 6000 platform at three developmental stages: primordia (SE6 -P), fruiting body differentiation (SE6 -F), and mature fruiting body (SE6 -M). Perform GO and KEGG enrichment analysis on differentially expressed genes at different developmental stages, and validate the sequencing results using qRT PCR. Results The assembled genome was 35.21 Mb, with a GC content of 48.10%, and contained 10,490 predicted protein -coding genes. A transcriptome data of 57.14 Gb was obtained, which was aligned to the reference genome to identify 2966 new genes. Differential gene expression analysis identified 360, 652, and 1057 annotated DEGs in SE6 -P vs SE6 -F, SE6 -F vs SE6 -M, and SE6 -P vs SE6 -M respectively. Notably, genes encoding phenylalanine ammonia lyase, glycoside hydrolase family, and aldo/keto reductase family have been consistently upregulated, playing an important regulatory role in growth and developmental process. KEGG pathway annotation further assigned PAL -encoding genes to the phenylalanine metabolism pathway (ko00360), supporting a role for PAL -mediated conversion of L -phenylalanine into downstream phenylpropanoid -related intermediates that may be associated with developmental progression. The accuracy of RNA Seq analysis was validated using qRT -PCR. Discussion Overall, this study provides and improved genome assembly and annotation for P. edulis , expands transcriptomic resources across key developmental stages, and establishes a solid genomic foundation for gene mapping, functional characterization, and molecular breeding effects in this species of P. edulis .