ArticleProceedings of the National Academy of Sciences of the United States of America2021
An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed, 179 citations in OpenAlex.
- What we (still don't) know about wood-degrading fungi: an overview of threats and utilization potentials.Applied microbiology and biotechnology · 2026Review
- Comparative Genomics Reveals Extensive Biosynthetic Diversity and Lineage-Specific Metabolic Potential AcrossJournal of fungi (Basel, Switzerland) · 2026Article
- Functional Characterization of Two Adjacent Oxygenase Genes,Journal of fungi (Basel, Switzerland) · 2026Article
- Comparative Phylogenomics Reveals Conserved Protoilludene Synthase Neighbourhoods and Unevenly Distributed Biosynthetic Gene Cluster Families in Armillaria.Journal of fungi (Basel, Switzerland) · 2026Article
- Tracing the origins of crmA megasynthase through lichen genomes.Current biology : CB · 2026Article
- Complex multicellularity is linked with expanded specialized metabolite production in microorganisms.Nature microbiology · 2026Article
- Bridging Discovery, Mechanism, and Application: An Integrated Strategy for Bioactive Natural Products.Molecules (Basel, Switzerland) · 2026Article
- Confrontations betweenApplied and environmental microbiology · 2026Article
- Equipped for success: genomes and metabolomes of the European Amanita muscaria are conserved in its novel South African range.The New phytologist · 2026Article
- Genetic Dereplication of MultipleJournal of natural products · 2026Article
- 2A peptides enable simplified discovery and heterologous production of fungal bioactive metabolites in Yarrowia lipolytica.Applied microbiology and biotechnology · 2026Article
- Large-scale multi-omics profiling reveals environmental and evolutionary drivers of fungal phylogeographic and metabolic diversity.Nature communications · 2026Article
- Chemical Signaling and Metabolomic Crosstalk in Endophytic Fungi-Medicinal Plant Symbioses for Natural Product Discovery and Sustainable Bioproduction.Metabolites · 2026Review
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- BGC-MAC and BGC-MAP: Attention-Based Models for Biosynthetic Gene Cluster Classification and Product Matching.Journal of chemical information and modeling · 2026Article
- The endophyteFrontiers in microbiology · 2026Article
- Exploration of inactive metabolic pathways in AntarcticIMA fungus · 2026Article
- Biodiversity-Driven Natural Products and Bioactive Metabolites.Plants (Basel, Switzerland) · 2025Review
- Review
- Paired-omics-based exploration and characterization of biosynthetic diversity in lichenized fungi.Microbial genomics · 2025Article
44 more citing papers are in PubMed but not listed here.
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5 authors at 2 institutions in 1 country.
Funding
Abstract
Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1,000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here, we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1,037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a >10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery.
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