The liquid fermentation of Antrodia cinnamomea is a promising alternative source for fungus production compared to the wildly grown fruiting body. Elicitation is a strong tool to enhance the productivity in microbial cells to obtain more compounds of interest. In this study, in order to improve the fungus growth and its terpenoids production, various vegetable oils were added in the fermentation broth of A. cinnamomea. It was found that corn oil from a group of vegetable oils exhibited the best effect on the biomass and triterpenoid content. After optimization, the initial addition of 1% (v/v) corn oil plus the inoculation of 10% (v/v) mycelia led to a maximum triterpenoid yield (532.3 mg L⁻¹), which was increased as much as fourfold compared to the blank control. Differential transcriptome analysis demonstrated that corn oil significantly enriched several metabolic pathways including glycolysis/gluconeogenesis, propanoate metabolism and transmembrane hydrophobins. The enriched pathways interacted with deferentially expressed genes (DEGs) induced by corn oil treatment. Our research provides a potential strategy for the large production of triterpenoids by the improved fermentation of A. cinnamomea.

Trametes versicolor is an important fungus with medicinal properties and a significant role in lignocellulose degradation. In this study, we constructed a high-quality chromosome-level genome of T. versicolor using Illumina, PacBio HiFi, and Hi-C sequencing technologies. The assembled genome is 47.42 Mb in size and contains 13,307 protein-coding genes. BUSCO analysis revealed genome and gene completeness results of 95.80% and 95.90%, respectively. Phylogenetic analysis showed that T. versicolor is most closely related to T. pubescens, followed by T. cinnabarina and T. coccinea. Comparative genomic analysis identified 266 syntenic blocks between T. versicolor and Wolfiporia cocos, indicating a conserved evolutionary pattern between the two species. Gene family analysis highlighted the expansion and contraction of genes in functional categories related to the biosynthesis of secondary metabolites, including several T. versicolor-specific genes. Key genes involved in lignocellulose degradation and triterpene production were identified within the CAZyme and CYP450 gene families. Transcriptomic analysis under dark and light conditions revealed significant changes in the expression of genes related to secondary metabolism, suggesting that light signals regulate metabolic pathways. A total of 2577 transporter proteins and 2582 membrane proteins were identified and mapped in the T. versicolor genome, and 33 secondary metabolite gene clusters were identified, including two light-sensitive triterpene biosynthesis clusters. This study offers a comprehensive genomic resource for further investigation into the functional genomics, metabolic regulation, and triterpene biosynthesis of T. versicolor, providing valuable insights into fungal evolution and biotechnological applications.

Cordyceps militaris, a model species in the genus Cordyceps, is widely distributed globally and is known for its significant medicinal value. It has been traditionally used in Chinese medicine to enhance immunity, alleviate fatigue, and treat tumors, among other therapeutic purposes. Here, we successfully assembled a telomere-to-telomere (T2T) level genome of C. militaris CH1 using PacBio HiFi and Hi-C technologies. The assembled genome is 32.67 Mb in size, with an N50 of 4.70 Mb. Gene prediction revealed a total of 10,749 predicted genes in the C. militaris CH1 genome, with a gene completeness of 99.20%. Phylogenetic analysis showed the evolutionary relationship between C. militaris CH1 and other Cordyceps species, suggesting that the divergence between this strain and C. militaris ATCC 34164 occurred approximately 1.36 Mya. Combined transcriptomic and metabolomic analyses identified 842 differentially expressed genes and 2052 metabolites that were significantly altered under light stress, primarily involving key pathways related to amino acid metabolism, purine metabolism, and secondary metabolite biosynthesis. Joint analysis of genes and metabolites revealed 79 genes coding for enzymes associated with the synthesis of adenine and adenosine, with the expression of 52 genes being upregulated, consistent with the accumulation trends of adenine and adenosine. Four gene clusters related to the synthesis of cordycepin were identified, with a significant upregulation of cns3 (FUN_003263), suggesting that light stress may promote cordycepin biosynthesis. This comprehensive analysis not only provides new insights into the genomics, metabolomics, and functional gene research of C. militaris CH1 but also offers a potential biological foundation for understanding the synthesis mechanisms of cordycepin and its efficient production.

Background: Coptis chinensis is a traditional medicinal plant rich in bioactive compounds like berberine, known for its antibacterial, anti-inflammatory, and antioxidant properties. This study aims to analyze the MYB transcription factor family in C. chinensis to better understand their roles in plant growth, development, metabolism, and stress responses. Methods: We employed bioinformatics to conduct a genome-wide identification of MYB genes in C. chinensis, followed by analyses of physicochemical properties, phylogenetic relationships, gene structures, chromosomal localization, conserved motifs, cis-acting elements, and expression patterns. Results were validated using qRT-PCR. Results: A total of 129 CcMYB genes were identified across nine chromosomes. Phylogenetic analysis categorized these genes into 19 subgroups, notably highlighting the S6 subgroup, which lacks counterparts in Arabidopsis. Comparative genomics revealed segmental duplication among gene pairs. Transcriptomic analysis indicated that CcMYB21, CcMYB40, CcMYB105, and CcMYB116 had high expression levels in stems. Importantly, CcMYB94 expression significantly increased under cadmium stress, suggesting its role in stress regulation. Conclusions: This study offers a comprehensive analysis of the MYB gene family in C. chinensis, underscoring the significance of MYB transcription factors in enhancing the plant’s medicinal value and stress tolerance, particularly against cadmium exposure. These insights pave the way for further exploration of specific MYB genes to improve stress resilience in C. chinensis.

Grifola frondosa, commonly known as turkey tail, is a valuable fungus with medicinal and culinary uses, rich in bioactive compounds like triterpenoid polysaccharides that contribute to health benefits. Here, we constructed a nearly complete genome of G. frondosa CH1 using Illumina, PacBio HiFi, and Hi-C sequencing technologies, resulting in a 35.74 Mb genome with 12,526 protein-coding genes. The genome spans 12 chromosomes, all with intact telomeric structures and no gaps. The BUSCO completeness scores of 95.1% and 99.1% for the genome and genes, respectively, indicate high assembly quality and high completeness of gene prediction. Phylogenetic analysis showed a close relationship between G. frondosa CH1 and Trametes cinnabarina. Transcriptomic analysis under varying light conditions showed changes in the expression of genes, especially those related to terpenoid synthesis, with several CAZymes and CYP450 genes also exhibiting light-induced variations. Ten triterpenoid secondary metabolite gene clusters were identified, three of which were light-sensitive, indicating that light exposure regulates triterpenoid metabolism. This study provides valuable data supporting the high-quality genome of G. frondosa and offers new insights into the light-induced regulation of its metabolism.