ArticleBMC genomics2022
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed, 80 citations in OpenAlex.
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- Cookbook for plant genome sequences.BMC genomics · 2026Review
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- First report of Aquitalea spp. From cave aquatic environments of Roraima Tepui, Guayana highlands.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.Frontiers in cellular and infection microbiology · 2026Article
- Pangenome-GWAS analysis ofCanadian journal of microbiology · 2026Article
- Pangenome graph analysis reveals evolution of resistance breaking in spinach downy mildew.PLoS biology · 2026Article
- Unveiling the Potential of Lentilactobacillus hilgardii in Malolactic Fermentation: Comparative Genomics and Fermentation Dynamics.Microbial biotechnology · 2025Article
- Multi-strain Analysis ofbioRxiv : the preprint server for biology · 2025Article
- PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data.Microbiology spectrum · 2025Article
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- Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe-Virus Coevolutionary System.Ecology letters · 2025Article
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- Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.Open forum infectious diseases · 2025Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundWith the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for "comparative pangenomics" that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants.
resultsApplied to 12,676 genomes across 12 microbial pathogenic species, we observed several shared resolution-specific patterns of genetic diversity: First, pangenome openness is associated with species' phylogenetic placement. Second, relationships between gene function and frequency are conserved across species, with core genomes enriched for metabolic and ribosomal genes and accessory genomes for trafficking, secretion, and defense-associated genes. Third, genes in core genomes with the highest sequence diversity are functionally diverse. Finally, certain protein domains are consistently mutation enriched across multiple species, especially among aminoacyl-tRNA synthetases where the extent of a domain's mutation enrichment is strongly function-dependent.
conclusionsThese results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.
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