ArticleNature microbiology2019
Evolutionary and functional patterns of shared gene neighbourhood in fungi.
Article in Nature microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 32 citations in OpenAlex.
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- TheIMA fungus · 2026Article
- A genomic perspective on fungal diversity and evolution.Nature reviews. Microbiology · 2025Review
- Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes.Microbiome · 2024Article
- Unlocking Fungal Potential: The CRISPR-Cas System as a Strategy for Secondary Metabolite Discovery.Journal of fungi (Basel, Switzerland) · 2024Review
- Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs.Microorganisms · 2024Article
- Functional Clustering of Metabolically Related Genes Is Conserved acrossJournal of fungi (Basel, Switzerland) · 2023Review
- Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces-Recommendations for Two New Genera and One Species.Journal of fungi (Basel, Switzerland) · 2022Article
- Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources.PLoS genetics · 2022Article
- Article
- Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation.Nature communications · 2021Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- Current Approaches for Advancement in Understanding the Molecular Mechanisms of Mycotoxin Biosynthesis.International journal of molecular sciences · 2021Review
- Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes amongJournal of fungi (Basel, Switzerland) · 2021Article
- Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery.Molecular biology and evolution · 2021Article
- Expanding the Knowledge on the Skillful YeastJournal of fungi (Basel, Switzerland) · 2021Review
- Article
- Fungal evolution: cellular, genomic and metabolic complexity.Biological reviews of the Cambridge Philosophical Society · 2020Article
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene clusters comprise genomically co-localized and potentially co-regulated genes that tend to be conserved across species. In eukaryotes, multiple examples of metabolic gene clusters are known, particularly among fungi and plants. However, little is known about how gene clustering patterns vary among taxa or with respect to functional roles. Furthermore, mechanisms of the formation, maintenance and evolution of gene clusters remain unknown. We surveyed 341 fungal genomes to discover gene clusters shared by different species, independently of their functions. We inferred 12,120 cluster families, which comprised roughly one third of the gene space and were enriched in genes associated with diverse cellular functions. Additionally, most clusters did not encode transcription factors, suggesting that they are regulated distally. We used phylogenomics to characterize the evolutionary history of these clusters. We found that most clusters originated once and were transmitted vertically, coupled to differential loss. However, convergent evolution-that is, independent appearance of the same cluster-was more prevalent than anticipated. Finally, horizontal gene transfer of entire clusters was somewhat restricted, with the exception of those associated with secondary metabolism. Altogether, our results provide insights on the evolution of gene clustering as well as a broad catalogue of evolutionarily conserved gene clusters whose function remains to be elucidated.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.