Cadmium is a major toxic heavy-metal pollutant considering their bioaccumulation potential and persistence in the environment. The hyperaccumulating ecotype of Sedum alfredii Hance is a Zn/Cd co-hyperaccumulator inhabiting in a region of China with soils rich in Pb/Zn. Investigations into the underlying regulatory mechanisms of molecular Cd tolerance are of substantial interest. Library screening for genes related to cadmium tolerance resulted in the discovery of a gene resembling the rubber elongation factor gene and here it is designated as SaREFl based on the preliminary bioinformatics analysis. The heterologous expression of SaREFl rescued the growth of a transformed Cd-sensitive strain (ycf1). Furthermore, Cd tolerance was enhanced in Arabidopsis plants expressing SaREFl with improvement in the fresh weight and root length of seedlings, as well as physiological indexes of adult plants. The investigation of gene expression profiles exposed to four different heavy metal treatments found that SaREFl exhibited different modes of transcriptional regulation upon heavy metal excess responding most strongly to Cd and the root was the plant organ most sensitive to this heavy metal. Screening a S. alfredii Hance cDNA library using the yeast two-hybrid technology with SaREFl as a bait led to the identification of five target genes possibly interacting with SaREFl and a gene named prenylated Rab acceptor 1 (PRA1) domain protein which was detected with a high frequency. Subcellular localization revealed that SaREFl mainly distributed in the cytosol. Our findings would further enrich the connotation of REF-like genes and provide theoretical assistance for the application in breeding heavy metal-tolerant plants.

This study investigated Morchella importuna strain degeneration during repeated subculturing and employed metabolomics, transcriptomics, and other techniques to explore its molecular mechanisms. Significant metabolic and transcriptional differences were observed between normal mycelia (NM) and degenerated mycelia (DG). Metabolomic analysis revealed 699 differentially expressed metabolites (DEMs) that were predominantly enriched in secondary metabolite biosynthesis pathways, particularly flavonoids and indole alkaloids. Total flavonoid content was markedly higher in NM than in DG, with most flavonoid compounds showing reduced levels in degenerated strains. Transcriptomic profiling revealed 2691 differentially expressed genes (DEGs), primarily associated with metabolic pathways and genetic information processing. Integrated analysis showed that metabolic dynamics were regulated by DEGs, with pyruvate metabolism being significantly enriched. The FunBGCeX tool identified biosynthetic gene clusters (BGCs) in the M. importuna genome, highlighting the critical role of the non-reducing polyketide synthase (NR-PKS) gene in flavonoid biosynthesis. This gene exhibited significantly downregulated expression in DG strains. These findings indicate that M. importuna degeneration resulted from systemic dysregulation of gene expression networks and metabolic pathway reorganization. The results presented herein also provide theoretical insights into degeneration mechanisms and potential prevention strategies for this edible fungus.

The Qinling Mountains are the geographic boundary between northern and southern China. In our current study, we investigated the biodiversity of macrofungi in the Qinling Mountains of Shaanxi and discovered a new species, Psilocybe ningshanensis. The phylogenetic tree shows its position in a group composed by P. hopii and P. mescaleroensis. They differ in some macro- and microscopic features, such as the presence or absence of an annulus or veil, the surface characteristics of the pileus, and the sizes and shapes of basidiospores and cheilocystidia. In addition, they are geographically distanced. P. ningshanensis was first discovered in Ningshan, China, whereas P. hopii and P. mescaleroensis were both found in the United States. In this article, we introduce the new species with illustrated description, ITS sequences, and comparisons with similar species.

Sporocarps of macrofungi support other diverse fungal species that are termed fungicolous fungi. However, the external environmental factors that affect the diversity and composition of fungicolous fungal communities remains largely unknown. In this study, the diversities, composition, and trophic modes of fungicolous fungal communities residing in host macrofungi from diverse habitats in the Qinling Mountains were analyzed. Additionally, the number of carbohydrate-active enzymes (CAZymes) encoded by saprophytic, pathogenic, and symbiotic fungi was also quantified and compared. The results revealed that the diversity and composition of fungicolous fungal communities varied with months of collection and the habitats of host fungi, and saprophytic fungi were more abundant on wood than on the ground. Meanwhile, it was also found that saprophytic fungi possessed higher abundances of cell-wall-degrading enzymes than pathogenic or symbiotic fungi. Based on the above findings, it was hypothesized that the greater abundance of saprophytic fungi on wood compared to the ground may be due to their possession of a more diverse array of enzymes capable of degrading wood cell walls, thereby allowing for more efficient nutrient acquisition from decaying wood.

Telomere-to-telomere (T2T) genomes provide a framework for resolving fungal chromosome architecture and lineage-specific evolution. We generated chromosome-complete assemblies of Coprinellus xanthothrix and C. saccharinus by integrating Oxford Nanopore, DNBSEQ, Hi-C, and RNA-seq data. Each genome comprised 13 gapless chromosomes with all 26 telomeres recovered; assembly sizes were 46.92 and 54.81 Mb, with BUSCO completeness of 99.20% and 99.10%, respectively. The larger C. saccharinus genome was primarily associated with greater retroelement content, whereas functional annotation profiles and CAZyme repertoires were broadly comparable between species. Phylogenomic analyses grouped C. xanthothrix with C. radians and C. saccharinus with C. micaceus, with estimated divergence times of 54.4 and 32.8 Ma, respectively. Both divergence events occurred within the Paleogene. Gene-family analyses identified lineage-specific expansions enriched in nucleotide metabolism, DNA replication and repair, glutathione metabolism, redox regulation, endocytosis, cytoskeletal organization, and cell-cycle processes. Synteny and Ks analyses further revealed chromosome-level rearrangements and lineage-specific small-scale duplication but no strong evidence of recent whole-genome duplication. Together, the temporal placement of these divergences and the associated genomic patterns raise a testable hypothesis that long-term climatic and vegetation reorganization, together with changes in plant-derived substrates and microhabitats, may have contributed to lineage establishment and ecological differentiation. However, because direct paleoecological evidence and functional validation are currently lacking, this proposed relationship should not be interpreted as causal. These chromosome-complete assemblies provide important resources for comparative genomics in Coprinellus and future experimental studies of saprotrophic adaptation.