ArticleGenome research2020
Accurate reconstruction of bacterial pan- and core genomes with PEPPAN.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- Pangenomic analysis reveals metabolic adaptation ofVirulence · 2026Article
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
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- Strategies for integrating whole-genome sequencing into antimicrobial resistance surveillance.BMC genomics · 2026Review
- A standardized core genome multilocus sequence typing and life identification number barcoding framework for globalMicrobial genomics · 2026Article
- Pathoadaptive evolution and clonal dissemination of community- associated methicillin-resistant Staphylococcus aureus in Egypt.BMC infectious diseases · 2026Article
- An optimized and integrated robust tool for pangenome generation.Functional & integrative genomics · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- Whole genome sequencing and molecular characterization of twoFrontiers in bioinformatics · 2026Article
- Comparative genomics reveals avian Acinetobacter baumannii as antimicrobial resistance reservoirs and bovine strains with elevated pathogenicity.Scientific reports · 2025Article
- PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks.Nature communications · 2025Article
- Revealing the spectrum of extended-core gene variation in the Escherichia coli pan-genome.BMC genomics · 2025Article
- Identification of a Novel Haloarchaeal SpeciesPolish journal of microbiology · 2025Article
- The Complete Genomes ofMicroorganisms · 2025Article
- KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings.Genome biology · 2025Article
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- Genetic landscape and evolution of Acinetobacter pittii, an underestimated emerging nosocomial pathogen.Communications biology · 2025Article
- Identification of essential genes by transposon insertion sequencing and genome-scale metabolic model construction inMicrobiology spectrum · 2025Article
- Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii.Nature communications · 2025Article
17 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses, including the calculation of trees based on accessory gene content or allelic differences between core genes. To test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pangenomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pangenome pipelines using both empirical and simulated data sets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pangenome of approximately 40,000 genes from 3052 representative genomes spanning at least 80 species of
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