ArticleFrontiers in microbiology2018
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of
Article in Frontiers in microbiology, 2018. 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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Who cites it
21 citing papers in PubMed, 50 citations in OpenAlex.
- Pangenome Analysis ofMicroorganisms · 2025Article
- Clostridium scindens: history and current outlook for a keystone species in the mammalian gut involved in bile acid and steroid metabolism.FEMS microbiology reviews · 2025Review
- Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments.Scientific reports · 2024Article
- Comparative genomics ofMicrobial genomics · 2023Article
- Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.Life (Basel, Switzerland) · 2023Review
- Phylogenomic analysis of theFrontiers in microbiology · 2023Article
- Genomic Insights ofFrontiers in microbiology · 2022Article
- Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns.Frontiers in plant science · 2022Review
- Nematophilic bacteria associated with entomopathogenic nematodes and drug development of their biomolecules.Frontiers in microbiology · 2022Review
- Phylogenetic systematics ofMicrobial genomics · 2021Article
- Article
- Diversity within species: interpreting strains in microbiomes.Nature reviews. Microbiology · 2020Review
- Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.The ISME journal · 2020Article
- PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.PLoS computational biology · 2020Article
- Estimating Pangenomes with Roary.Molecular biology and evolution · 2020Article
- First Steps in the Analysis of Prokaryotic Pan-Genomes.Bioinformatics and biology insights · 2020Review
- Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.BMC genomics · 2019Article
- Improved genome ofPeerJ · 2019Article
- Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.BMC genomics · 2018Article
- Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions.Genome biology and evolution · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria
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