Construction of the genome of Hericium coralloides, a species of edible mushroom, and identification of the genes involved in terpenoid biosynthesis can determine the biology and genetics of terpenoids. The present study describes the assembly of a high-quality chromosome-scale genome of H. coralloides using Pacbio HiFi sequencing and Hi-C technology. This genome consisted of 13 chromosomes, a total size of 43.6 Mb, contigs of N50 3.6 Mb, GC content at 54%, and BUSCOs integrity of 96.9%. Genes associated with terpenoid biosynthesis were predicted by KEGG enrichment analysis and homologous alignment. The Her011461 and Her008335 genes, encoding proteins in the terpenoid backbone synthesis pathway, were found to encode geranylgeranyl pyrophosphate and farnesyl diphosphate synthases, key enzymes in the biosynthesis of geranylgeranyl diphosphate, a precursor of several diterpenoids. Her011463 was found to be involved in regulating diterpene cyclase. The Her005433, Her006724, Her010605, and Her010608 genes were found to encode sesquiterpene synthesis. Most of these genes were more highly expressed in dikaryotic mycelia than in the primordium and fruiting bodies, indicating that terpenoids may be more abundant in dikaryotic mycelia. To our knowledge, this study is the first to assemble the H. coralloides genome at the chromosome scale and to identify the genes involved in terpenoid biosynthesis.

The key agronomic traits for evaluating the vegetative and reproductive growth capacities of edible mushrooms are the abundance of aerial mycelia and stipe length. These traits directly affect mycelial vitality and fruiting body yield. However, the molecular mechanisms regulating these traits are poorly understood. In this study, Flammulina filiformis mutant with a T-DNA insert exhibited sparse aerial mycelia and longer stipes, which were caused by upregulated expression of a novel self-activating protein FfGH79. The FfGH79 protein, consisting of 238 amino acids and with a relative molecular mass of 27.45 kDa, was localized in the nucleus, but lacked known structural domains. Alignment of homologous proteins from 12 fungi that produce fruiting bodies identified four typical alpha helices in the N-terminal region and one beta turn in the C-terminal region, both of which were conserved tertiary structures. FfGH79 gene overexpression and knockdown strains were constructed to confirm that this gene negatively regulates mycelial branch distance, which results in sparse aerial mycelia. Further, FfGH79 gene positively regulates stipe elongation ability, thereby increasing fruiting body yield. Transcriptomic analysis revealed that most lectin-like and reactive oxygen species catabolism genes were downregulated in the gh79 mutant. These findings provide a new research target for understanding mycelial growth, the mechanisms of fruiting body development, and molecular breeding of edible mushrooms.