ArticleNature methods2025
De novo discovery of conserved gene clusters in microbial genomes with Spacedust.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Fast, flexible gene cluster family delineation with IGUA.Nucleic acids research · 2026Article
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.Nucleic acids research · 2026Article
- Characterization of syntons across bacterial genomes using non-redundant genomic contexts.microLife · 2026Article
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- Synteny plot quality control with SyntenyQC.Bioinformatics (Oxford, England) · 2025Article
- The Prevalence and Diversity of Marine Toxin-Antitoxin Systems.Marine drugs · 2025Article
- In silico approaches for discovering microbial antiviral defense systems.Briefings in bioinformatics · 2025Review
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Authors and funding
3 authors.
Funding
Abstract
Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with known biological processes and molecular functions presents a major bottleneck. In prokaryotes and viruses, evolution favors keeping genes participating in the same biological processes colocalized as conserved gene clusters. Conversely, conservation of gene neighborhood indicates functional association. Here we present Spacedust, a tool for systematic, de novo discovery of conserved gene clusters. To find homologous protein matches, Spacedust uses fast and sensitive structure comparison with Foldseek. Partially conserved clusters are detected using novel clustering and order conservation P values. We demonstrate Spacedust's sensitivity with an all-versus-all analysis of 1,308 bacterial genomes, identifying 72,843 conserved gene clusters containing 58% of the 4.2 million genes. It recovered 95% of antiviral defense system clusters annotated by the specialized tool PADLOC. Spacedust's high sensitivity and speed will facilitate the annotation of large numbers of sequenced bacterial, archaeal and viral genomes.
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