ArticleMolecular biology and evolution2020
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 53 citations in OpenAlex.
- Telomere-to-Telomere Genomes Reveal that Multiscale Evolution Shapes the Largest Metabolic Arsenal of Diaporthe Fungi.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An Exploratory LC-HRMS Metabolomics Study of Culture Medium-Dependent Metabolic Variation and Bioactivity in Ten Fungal Strains.International journal of molecular sciences · 2026Article
- Chemical Signaling and Metabolomic Crosstalk in Endophytic Fungi-Medicinal Plant Symbioses for Natural Product Discovery and Sustainable Bioproduction.Metabolites · 2026Review
- Metabolite diversity of Microcystis strains shows tight correspondence to genotype and may contribute to ecotype specificities.Communications biology · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
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- Generalized Gene Cluster Detection Using CLOCI.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational Approaches for Discovering Virulence Factors inJournal of fungi (Basel, Switzerland) · 2025Review
- Article
- Genome mining reveals the distribution of biosynthetic gene clusters in Alternaria and related fungal taxa within the family Pleosporaceae.BMC genomics · 2025Article
- Article
- A Biosynthetic and Taxonomic Atlas of the Global Lichen Holobiont.Environmental microbiology · 2025Article
- Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces.BMC genomics · 2025Article
- Genetic sequencing of the airborne fungal spectrum and air quality at a public hospital in Mexico City.PLOS global public health · 2025Article
- CLOCI: unveiling cryptic fungal gene clusters with generalized detection.Nucleic acids research · 2024Article
- Comparative Genomics of Fungi in Nectriaceae Reveals Their Environmental Adaptation and Conservation Strategies.Journal of fungi (Basel, Switzerland) · 2024Article
- Universal signatures of transposable element compartmentalization across eukaryotic genomes.bioRxiv : the preprint server for biology · 2024Article
- First Genome Sequence of the Microcolonial Black FungusMicroorganisms · 2024Article
- Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters.Nucleic acids research · 2023Article
- Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle.International journal of molecular sciences · 2023Review
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Authors and funding
8 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.
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