Buchwaldoboletus xylophilus is a rare saprotrophic edible mushroom in the Boletaceae and is the second bolete species to have been successfully cultivated artificially, yet its developmental molecular regulation remains unexplored. We integrated RNA-seq transcriptomics and untargeted LC-MS/MS metabolomics across five developmental stages (A–E), applying differential expression, alternative splicing, ceRNA network construction, WGCNA, machine learning, consensus clustering, and O2PLS joint modelling. Transcriptomic analysis revealed that the mycelium-to-primordium transition (stage A to C) showed the most drastic reprogramming, with 2233 differentially expressed genes, while metabolomic comparison between stage A and E revealed overwhelmingly upregulated metabolites (184 up vs. 10 down), indicating asymmetric regulation between the two omics layers. Notably, mutually exclusive exon splicing events exhibited high functional significance, and all top ceRNA hubs were lncRNAs. Unsupervised consensus clustering validated the molecular distinctness of the sampled stages. Metabolite enrichment highlighted antioxidant functions and ABC transporter pathways, and O2PLS integrative modelling confirmed a strong shared developmental signal between transcriptome and metabolome. This study provides the first multidimensional molecular atlas for B. xylophilus, revealing a non-linear developmental programme, transcriptome–metabolome decoupling, and a central role of antioxidant defence throughout development. Our findings offer mechanistic clues regarding the evolutionary transition from ectomycorrhizal to saprotrophic lifestyles in the Boletaceae and establish a multi-omics foundation for the molecular breeding of this emerging edible and medicinal mushroom.

Plant pathogens pose a severe threat to global agricultural production, and their pathogenicity is closely linked to the biosynthesis of secondary metabolites. Basidiomycete within the family Ustilaginaceae represent significant plant pathogens, among which Ustilago maydis, as a model species, has been extensively studied for its secondary metabolites. However, the biosynthetic potential of other species within this family remains poorly understood. In this study, we conducted whole-genome bioinformatic analyses of 16 Ustilaginaceae species, including U. maydis, to systematically identify the distribution of biosynthetic gene clusters (BGCs), core gene domain compositions, and interspecies similarities. A total of 181 predicted BGCs were identified, averaging approximately 11 per species. BGCs for mannosylerythritol lipids (MELs), siderophores, and itaconic acid, as well as the melanin-associated genes pks1 and pks2, were widely distributed across most species. Conversely, an additional melanin biosynthetic gene cluster was found exclusively in U. maydis strain 521, indicating species-specific occurrence. Furthermore, this study identified a novel class of polyketide synthase (PKS) gene clusters with uncharacterized functions across 15 species, exhibiting high sequence and structural conservation between species. These findings reveal the rich metabolic diversity and species-specific biosynthetic potential of Ustilaginaceae, and by using U. maydis as a reference model, we highlight several BGCs (e.g., for MELs, siderophores, itaconic acid, and melanin) that are known to contribute to virulence or pathogenicity in plant hosts. This provides new insights into their pathogenic mechanisms.

Pappia fissilis is a white-rot fungus capable of colonizing lignocellulosic substrates and decomposing plant cell wall components, and is likely involved in the degradation of woody debris and carbon cycling in forest ecosystems. A variety of lanostane-type triterpenoids and other bioactive compounds have been isolated from its fruiting bodies, pointing to potential value in natural product development. However, previous studies on this species have been largely confined to taxonomy, mitochondrial genomics, and chemical profiling of fruiting bodies, leaving its genomic features and the genetic underpinnings of wood decay and secondary metabolism poorly characterized. Here, we leveraged a hybrid sequencing strategy combining PacBio HiFi, Illumina, and Hi-C data to generate a chromosome-level genome assembly and annotation for P. fissilis, and conducted comprehensive phylogenomic, comparative genomic, CYP450, CAZyme, and biosynthetic gene cluster (BGC) analyses, which report the first genome resource for this species. The assembled genome spans 38.63 Mb, with 97.52% of the sequence anchored to 11 chromosomes, a BUSCO completeness of 95.4%, and 9499 predicted protein-coding genes. Phylogenomic analysis recovered P. fissilis as sister to a clade comprising Phlebia radiata and P. brevispora, with an estimated divergence time of approximately 53.17 Mya. The genome contains 153 CYP450 genes, 436 CAZyme genes, and 26 candidate BGCs harboring a total of 30 core biosynthetic genes (22 terpene, 5 T1PKS, 1 T3PKS, 2 $\beta$-lactone); these core genes are predominantly associated with terpene biosynthesis, and also encompass diverse types of polyketide synthase (PKS) genes as well as genes implicated in $\beta$-lactone biosynthesis. Collectively, these results establish a chromosome-level reference for investigating the genome evolution, wood-decay ecology, and secondary metabolic potential of P. fissilis, and lay the groundwork for future functional characterization of candidate biosynthetic genes and their associated natural products.