Cited by 393Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsBacterial Genetics and Biotechnology

The DOI matches its Crossref record; 131 of the 131 references it cites were found in a registry or an index.

The Ecology and Evolution of Pangenomes

Open access

Brockhurst, Michael A., Harrison, Ellie, Hall, James P.J., Richards, Thomas, McNally, Alan, MacLean, Craig·2019·Current Biology

DOI 10.1016/j.cub.2019.08.012

Open this paper in CoChat — free account Open PDF

Abstract

Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept. The pangenome is defined as the set of all the genes present in a given species and can be subdivided into the accessory genome, present in only some of the genomes, and the core genome, present in all the genomes. Pangenomes arise due to gene gain by genomes from other species through horizontal gene transfer and differential gene loss among genomes, and have been described in both prokaryotes and eukaryotes. Our current view of pangenome variation is phenomenological and incomplete. In this review, we outline the mechanistic, ecological and evolutionary drivers of and barriers to horizontal gene transfer that are likely to structure pangenomes. We highlight the key role of conflict between the host chromosome(s) and the mobile genetic elements that mediate gene exchange. We identify shortcomings in our current models of pangenome evolution and suggest directions for future research to allow a more complete understanding of how and why pangenomes evolve.

Integrity signals

Registry

Crossref · 10.1016/j.cub.2019.08.012

Cites

131 of 131 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316
Mobile Genetic Elements Associated with Antimicrobial Resistance
Partridge, S. R., Kwong, S. M., Firth, N., & Jensen, S. O. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00088-17 · Cited by 2,751
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”
Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506758102 · Cited by 2,728
Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria
Thomas, C. M., & Nielsen, K. M. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1234 · Cited by 2,194
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
Perna, N. T., Plunkett, G., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., et al. (2001) · Nature · doi:10.1038/35054089 · Cited by 2,035
Effective population size and patterns of molecular evolution and variation
Charlesworth, B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2526 · Cited by 1,743
CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA
Marraffini, L. A., & Sontheimer, E. J. (2008) · Science · doi:10.1126/science.1165771 · Cited by 1,642
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
Welch, R. A., Burland, V., Plunkett, G., Redford, P., Roesch, P. L., Rasko, D. A., Buckles, E. L., Liou, S., Boutin, A., Hackett, J. D., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252529799 · Cited by 1,523
RNA Interference: Biology, Mechanism, and Applications
Agrawal, N., Dasaradhi, P. V. N., Mohmmed, A., Malhotra, P., Bhatnagar, R. K., & Mukherjee, S. K. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.4.657-685.2003 · Cited by 1,373
Systematic discovery of antiphage defense systems in the microbial pangenome
Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., & Sorek, R. (2018) · Science · doi:10.1126/science.aar4120 · Cited by 1,242

Flagged first, then by citations

Show all 131 references

Sorted by citations

Items 301–393 of 393

Additional file 5 of Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill
Wang, Y., Ma, L., He, J., Liu, Z., Weng, S., Wang, L., He, J., & Guo, C.-J. (2021) · Figshare · doi:10.6084/m9.figshare.16862785
Slings and arrows: sRNAs mediate intragenomic competition
Ferrell, M. J., & Waters, C. M. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.04.013
Plasmids: Tiny pieces with high efficacy (Review)
Kokaz, O. F., Muhammad, A. A., & Alkhuzaie, M. M. (2024) · Journal of Medical Genetics and Clinical Biology · doi:10.61796/jmgcb.v1i3.383
Commensal or pathogen: computationally vectorizing microbial genomes for de novo risk assessment and virulence feature discovery in Klebsiella pneumoniaePreprint
Beck, K. L., Agarwal, A., Halpin, A. L., McDonald, L. C., McKay, S. L., Kent, A. G., Kaufman, J. H., Mukherjee, V. V., Elkins, C. A., & Seabolt, E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.13.593956
Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer
Hong, J., Xue, W., & Wang, T. (2025) · eLife · doi:10.7554/elife.99593.3
A small RNA derived from the 5’ end of the IS200 tnpA transcript regulates multiple virulence regulons in Salmonella TyphimuriumPreprint
Trussler, R. S., Scherba, N. Q., Ellis, M. J., Förstner, K. U., Albert, M., Westermann, A. J., & Haniford, D. B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.26.600842
Reviewer #2 (Public Review): The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
(2024) · eLife · doi:10.7554/elife.97870.1.sa1
Reviewer #1 (Public Review): The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
(2024) · eLife · doi:10.7554/elife.97870.1.sa2
eLife Assessment: The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
Kana, B. D. (2024) · eLife · doi:10.7554/elife.97870.1.sa3
Author response: The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference
Behruznia, M., Marin, M. G., Farhat, M. R., Thomas, J. C., Domingo-Sananes, M. R., & Meehan, C. J. (2024) · eLife · doi:10.7554/elife.97870.1.sa0
Insights into the Roles of Giant Starships of Diversity in Fungal Genomes
Harish, J., Karan, R., P, M. P. B., Lakshmeesha, R., Dodmani, B. A., Vamsidharreddy, N., Vineeth, M., Shree, D., Chethan, D., & Kumar, P. V. D. (2024) · PLANT CELL BIOTECHNOLOGY AND MOLECULAR BIOLOGY · doi:10.56557/pcbmb/2024/v25i11-128837
Innate antiviral systems are major defensome components that drive prophage distribution in Acinetobacter baumanniiPreprint
Moreno-Rodríguez, A., Rubio, A., Garzón, A., Smani, Y., & Pérez‐Pulido, A. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.26.620419
Emergence of alternative stable states in gene exchange communitiesPreprint
Hong, J., Xue, W., & Wang, T. (2024) · eLife · doi:10.7554/elife.99593.1
Unraveling the Gardnerella Pangenome: Insights into Genetic Diversity, Virulence, and Antibiotic ResistancePreprint
Teixeira, P., Sousa, M., Ribeiro, T. G., Grosso, F., & Peixe, L. M. S. V. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.03.641253
Climate-Driven Shift in Plant-Microbe Dynamics: A Comprehensive Review
Singh, N. (2025) · Microorganisms for sustainability · doi:10.1007/978-981-96-3748-5_3
Beyond Mendel and Morgan to the dynamic genome
Golubovsky, M. D. (2025) · VAVILOVIA · doi:10.30901/2658-3860-2024-3-o1
Pangenomes: Unveiling Genetic Diversity Across Populations and Beyond
Bilal, M., & Battistuzzi, F. U. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15750-9.00139-7
The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of differencePreprint
Behruznia, M., Marin, M. G., Whiley, D. J., Farhat, M. R., Thomas, J. C., Domingo-Sananes, M. R., & Meehan, C. J. (2025) · eLife · doi:10.7554/elife.97870.2
How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens
Bellinzona, G., Biffignandi, G. B., Brilli, M., Baldanti, F., Sassera, D., & Gaiarsa, S. (2025) · Microbial Genomics · doi:10.1099/mgen.0.001459
Microbial diversity and functional potential of the Halobates melleus (Heteroptera: Gerridae) microbiome from the Red Sea coastline
Escobar-Prieto, J. D., Goethem, M. W. V., Vernooij, B., Antony, C. P., Cheng, L., Mishra, H., Marasco, R., & Daffonchio, D. G. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00761-y
The Pangenome Variability Index: A Quantitative Measure for Assessing Gene Content Diversity in Microbial Genomes
Munteanu, V., Leahu, A., Ciorbă, D., Catlabuga, E., Drabcinski, N., Dubciuc, D., Iapăscurtă, V., & Bostan, V. (2025) · World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany · doi:10.1007/978-3-032-06497-4_26
Pangenomics for studying plant population genetics
Ananda-Lekshmi, L.-D., Ariharasutharsan, G., Khan, M. A., & Karthikeyan, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26791-8.00019-4
Pangenomes empower the investigation of biological adaptations
Liu, Y., Kainer, D., Jannah, A. L., & Cooper, M. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26791-8.00018-2
Pangenomics for developing fungal disease-resistant plants
Elbouzidi, A., Haddou, M., Taibi, M., Baraich, A., & Addi, M. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26791-8.00016-9
Genomic plasticity of the Azospirillum genus in a biotechnological contextPreprint
Henaut-Jacobs, S., Rimes-Casais, F. F., Quintanilha‐Peixoto, G., Mota, G. P., Rodrigues, B. D. C., Oliveira-Pinheiro, I., da Fonseca, R. N., Olivares, F. L., Etienne, R. S., & Venâncio, T. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.16.682878
Life history and population biology
(2023) · CSIRO Publishing eBooks · doi:10.1071/9781486314935.bk08025_part2
Genomic analysis of the probiotic candidate Bifidobacterium bifidum strain 900791 in the context of the B. bifidum pangenomePreprint
Cárdenas, J. P., Vidal‐Veuthey, B., Meza, K., Almonacid, D. E., & Gutkevich, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.10.687612
Human genome project and current status
Chaudhary, A., Kritika, Bharmaik, A., & Mittal, S. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-21980-1.00019-x
The evolutionary genomics of incipient endosymbiosis in wild rhizobia bacteriaPreprint
Montoya, A. P., Jensen, K. T., Griffitts, J. S., & Porter, S. S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.03.692210
Additional file 1 of Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Colquhoun, R. M., Hall, M. B., Lima, L., Roberts, L. W., Malone, K. M., Hunt, M., Letcher, B., Hawkey, J., George, S., Pankhurst, L. J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16620759
Additional file 2 of Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China
Chen, H., Yin, Y., van Dorp, L., Shaw, L. P., Gao, H., Acman, M., Yuan, J., Chen, F., Sun, S., Wang, X., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16901002
Additional file 1 of Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill
Wang, Y., Ma, L., He, J., Liu, Z., 翁少萍, Wang, L., He, J., & Guo, C. (2021) · Figshare · doi:10.6084/m9.figshare.16862773
Additional file 2 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609241
Additional file 4 of Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill
Wang, Y., Ma, L., He, J., Liu, Z., 翁少萍, Wang, L., He, J., & Guo, C. (2021) · Figshare · doi:10.6084/m9.figshare.16862782
Additional file 1 of A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes
Guo, J., Pang, E., Song, H., & Lin, K. (2021) · Figshare · doi:10.6084/m9.figshare.14691768
Additional file 7 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609256
Additional file 3 of Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill
Wang, Y., Ma, L., He, J., Liu, Z., 翁少萍, Wang, L., He, J., & Guo, C. (2021) · Figshare · doi:10.6084/m9.figshare.16862779
Additional file 5 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609250
Additional file 2 of A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome
Zhang, D., Zhang, J., Kalimuthu, S., Liu, J., Song, Z., He, B.-B., Cai, P., Zhong, Z., Feng, C., Neelakantan, P., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22705970
Additional file 1 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609238
Additional file 3 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609244
Additional file 4 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609247
Additional file 1 of Assessment of assumptions underlying models of prokaryotic pangenome evolution
Sela, I., Wolf, Y. I., & Koonin, E. V. (2021) · Figshare · doi:10.6084/m9.figshare.13844032
Additional file 2 of Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill
Wang, Y., Ma, L., He, J., Liu, Z., 翁少萍, Wang, L., He, J., & Guo, C. (2021) · Figshare · doi:10.6084/m9.figshare.16862776
Additional file 2 of Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Colquhoun, R. M., Hall, M. B., Lima, L., Roberts, L. W., Malone, K. M., Hunt, M., Letcher, B., Hawkey, J., George, S., Pankhurst, L. J., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16620762
Additional file 6 of Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome
Hyun, J. C., & Palsson, B. O. (2024) · Figshare · doi:10.6084/m9.figshare.26609253
Pangenomics for combating plant diseases
Kalaichelvi, K., A, S. E. A., Karthiba, L., Nakkeeran, S., Vanitha, S., Kamalakannan, A., Renukadevi, P., Anantha Raju, P., Raveena, R., Jeya Rani, M., et al. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26791-8.00014-5
Molecular insights into plant-pest interactions based on pangenomics and functional genomics
Assouguem, A., Kallali, N. S., Boutagayout, A., Goura, K., Radi, M., Kouighat, M., Laasli, S.-E., Mokrını, F., Farhaoui, A., & Lahlali, R. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26791-8.00024-8
Negative Frequency‐Dependent Selection Promotes Strain Structure in a Plant Pathogen
Li, S., Laderman, E., Märkle, H., Yang, Y., Bergelson, J. M., & Pascual, M. (2026) · Ecology Letters · doi:10.1111/ele.70304
Motile and non-motile Listeria species adopt distinct genomic and ecological strategies to achieve broad geographic ranges in soilPreprint
Goh, Y.-X., Hepp, S. L., Cummings, K. J., Wiedmann, M., & Liao, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.08.698536
Integrative mobilizable elements are pervasive throughout PseudomonadotaPreprint
Perta, A. M., Nadal-Molero, F., Cabello‐Yeves, P. J., García‐González, N., Gónzález‐Candelas, F., & Fillol-Salom, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.12.698999
GLADE: Accurate inference of Gains, Losses, Ancestral genomes, and Duplication Events for comparative genomicsPreprint
Belcher, L. J., & Kelly, S. L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.702036 · Cited by 1
Horizontal transfer of post-translational modifiers brings evolutionary opportunity and challenges to a conserved translation factor
Brewer, T. E., Kielkowski, P., Stritzel, J., Meier-Rosar, F., Schlundt, A., & Lassak, J. (2026) · BMC Biology · doi:10.1186/s12915-026-02531-9
Evolutionary dynamics of type VI secretion systems in fruit fly-associated Enterobacter
Mokhtar, N. B., Stathopoulou, P. M., Asimakis, E. D., Augustinos, A. A., Salgueiro, J., Alleck, M., Sookar, P., Dembilio, Ó., Segura, D. F., & Tsiamis, G. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1755534
From genome to lifestyle: adaptive strategies of Pseudomonas sp. AU10 and its Antarctic lineage
García-Laviña, C. X., Smircich, P., & Castro‐Sowinski, S. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.02470-25
Replaying the Tape: Comparative Genomics of Color Pattern in HeliconiusPreprint
Lawrence, C. G., Arias, C. F., McMillan, W. O., & Rubenstein, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.23.713665
Microbial Omics
Erözden, A. A., Tavşanlı, N., Çalışkan, M., & Arıkan, M. (2026) · Progress in molecular and subcellular biology · doi:10.1007/978-3-032-11438-9_10
Comparative genomics reveals synteny-guided remodeling of carbohydrate-foraging and intrinsic resistance in an ocular Chryseobacterium isolate, NG-CE01
Hassan, F., TÜRKYILMAZ, S., & El-Mahdy, T. S. (2026) · BMC Microbiology · doi:10.1186/s12866-026-04950-8
Conceptualisation et exploitation d’un graphe de pangénome partitionné comme représentation compacte de la diversité du répertoire génique des espèces procaryotes
Gautreau, G. (2020) · theses.fr (ABES) · doi:10.70675/d5c3a7fezdc60z410fza79cz2ed2c937aa11
Tools for massive bacterial comparative genomics : Development and Applications
Perrin, A. (2022) · theses.fr (ABES) · doi:10.70675/a061aa00z774bz40c5zb870zba9af4cac64b
Methods for genome-wide structural variation inference in skimming data using graph pangenome
Dang, T. M. N. (2022) · doi:10.70675/725d5452z1adcz4104zb78dz430950e41644
Étude du pangénome d’une population bactérienne structurée : vers une nouvelle compréhension de l’origine des variations intra-génomiques
Gardon, H. (2021) · theses.fr (ABES) · doi:10.70675/6bb87acez122bz48ebza8c7zd74e2330330d
Caractérisation génomique et phylogénomique de Mycobacterium avium ssp. paratuberculosis : portrait des souches qui circulent dans les élevages laitiers du grand Ouest de la France
Condé, C. (2022) · doi:10.70675/3fa6aa39z27baz4540za2b0z28c74219a0bb
Origin and evolutionary trajectory of microRNA genes in Arabidopsis species
Pavan, F. (2024) · doi:10.70675/ab5c4ecez5ac1z4c92zadffz8f16ce2c54c7
Comparative Genomic Study of Candida Albicans Highlights its Pangenome as a Genomic Window into Eukaryotic Biodiversity
Ramírez-Mata, N., Mora-Cubillo, P., & Molina-Mora, J. A. (2025) · IEEE International Conference on BioInspired Processing (BIP) · doi:10.1109/bip68491.2025.11489085
Staphylococcus epidermidis Genomic Plasticity Modulates Horizontal Gene TransferPreprint
Tran, M., Viera, A. J. H., Rosu, J. A., Tran, P., Goldman, D. A., & Mo, C. Y. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.01.722213
Pangenomes
Pramitha, L., Rana, S., Jeeva, G., Devasena, N., Aananthi, N., & Muthamilarasan, M. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40401-6.00019-4
Genomic insights into intra-specific differentiation and potential evolution of antibiotic resistance/virulence factor genes in Klebsiella oxytoca
Wang, Y., Han, H., Qing, Y., Wei, G., & Zhang, X. (2026) · Microbial Pathogenesis · doi:10.1016/j.micpath.2026.108600
Three novel Rothia species associated with Antarctic birds harbour novel biosynthetic gene clusters
Koublová, V., Musilová, J., Sedlář, K., Spacek, P., Vives, J., Staňková, E., Šedo, O., Králová, S., Sehnal, L., Sedláček, I., et al. (2026) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiag056
Using protein language models for pangenome constructionPreprint
Larsen, N. J., Charusanti, P., Webel, H. E., Ohl, L., Blin, K., & Frellsen, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.04.730042
Shotgun metagenomics uncovers novel features of the cyanobacterial community in a large, shallow lake in Central Italy
Salmaso, N., Cerasino, L., Brizio, M. D., Pindo, M., & Boscaini, A. (2026) · Hydrobiologia · doi:10.1007/s10750-026-06250-8
A structural backbone with sequestered plasticity organizes the Escherichia coli pangenome
Lu, Y.-F., Zuo, G., & Zhi, X. (2026) · mSystems · doi:10.1128/msystems.00207-26
Genome-wide analysis of biosynthetic gene clusters reveals hidden metabolic diversity in bacterial fish pathogens
Olymon, K., Bhattacharjee, I., Roy, N., Sabari, R. S., Dey, U., Teronpi, V., & Kumar, A. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-05087-6
Ecological plasticity of Halanaerobium microorganisms across terrestrial saline to hypersaline subsurface environments
He, Y., Wang, X., Li, S. Y., Zhang, C. L., Xu, M., Zhou, Y., Sanford, R. A., Liang, R., Zhu, Y., Yang, D., et al. (2026) · Microbiology Spectrum · doi:10.1128/spectrum.01381-26
In-silico analysis of Bifidobacterium bifidum strain 900791 genome in the context of the B. bifidum pangenome
Cárdenas, J. P., Vidal‐Veuthey, B., Meza, K., Almonacid, D. E., & Gutkevich, A. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1744409
Synteny-aware microbial pangenome graphs reveal blueprints of genomic variationPreprint
Henoch, A., Sever, M., Tucker, S. J., Trigodet, F., Veseli, I., Chang, T., McInerney, J. O., Söylev, A., Freel, K. C., Rappé, M. S., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.03.736256 · Cited by 1
Genomic structural variation rescues a classic biological invader from a population bottleneck
Osborne, C. A., Foote, B. M., Fleck, S. J., Waterman, H. M., Chang, S. L., Nafus, M. G., Bellinger, M. R., Gray, L. N., & Krabbenhoft, T. J. (2026) · Science Advances · doi:10.1126/sciadv.aed3656 · Cited by 1
Phylogenomics and comparative genomics of the genus Erwinia reveal taxonomic inconsistencies and evolutionary diversificationPreprint
Maurya, N., Dobhal, S., Sundin, G. W., Rodoni, B. R., Stack, J. P., & Arif, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.06.743344
Genome-scale analysis of Mycobacteroides abscessus clinical isolates from a university hospital
Sirichoat, A., Oungbamnet, C., Hinwan, Y., Nithimongkolchai, N., Sawaswong, V., Chitcharoen, S., & Faksri, K. (2026) · Journal of King Saud University - Science · doi:10.25259/jksus_1773_2025
Comparative genomics of ESKAPE pathogen species: Integrating pan-genome architecture, antimicrobial resistance, and virulence factor repertoires
Singh, S., & Kumar, P. (2026) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2026.109359
Pan-genomic analysis of the multi-drug resistant strains of Mycobacterium tuberculosis
Anandan, N., Venkatachalam, R., & Sundar, S. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-05219-y
Ecological theory sheds light on plasmid diversity and dynamics
Tuffet, R., Acacia, E., Coluzzi, C., Charpentier, X., Koffel, T., & Venner, S. (2026) · PLoS Biology · doi:10.1371/journal.pbio.3003918
Oxford Nanopore Sequencing of Clinical DNA for Identification and Comparative Genomic Analysis of Erysipelothrix piscisicarius
Kajeekul, R., Wongsurawat, T., Kruasuwan, W., Sawankatat, P., Nimsamer, P., Arigul, T., Riwlord, A., Jenjaroenpun, P., & Kerdsin, A. (2026) · Transboundary and Emerging Diseases · doi:10.1155/tbed/5654145
Reduced recombination relative to mutation characterizes dominant circulating clones of Mycobacterium abscessusPreprint
Zhu, C., Zhou, Y., Ni, M., Huang, Z., Wang, Z., Zhu, J., & Li, W. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.03.749045
Comparative pangenomics of the Corynebacterium kroppenstedtii complex reveals species structure and accessory genome diversity
Zhou, X., Zhang, Y., Qiu, Y., & Feng, L. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1947083
A metal(loid)-tolerant Paenibacillus vandeheii strain from mine tailings soil reveals traits associated with adaptation to metallurgical contamination
Mestre, A. Z., Muñoz-Ramírez, Z. Y., Carrillo‐Campos, J., Delgado-Gardea, M. C. E., Infante‐Ramírez, R., & González-Escobedo, R. (2026) · Earth Critical Zone · doi:10.1016/j.ecz.2026.100098
Deciphering the Genome Evolution and Cryptic Biosynthetic Potential in Rare Lentzea spp.
Hua, L. S., Jiao, X., Huang, W., Fan, X., Sun, W., Xu, J., Zhou, L., Niu, W., Luo, X., Wan, C., et al. (2026) · Antibiotics · doi:10.3390/antibiotics15100967
Comparison of three routine methods for the identification of Kerstersia gyiorum from routine diagnostics and review of the literature
Purschwitz, L., Bunk, B., & Schröttner, P. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1901541
Large-scale genome re-annotation uncovers pathogen-specific lncRNA regulators of fungal growth and virulence
Gao, R., Liu, Z., Tang, H., Wang, N., Xue, X., Lu, L., & Zhang, Y. (2026) · PLoS Pathogens · doi:10.1371/journal.ppat.1014681
mGem: Bacterial aversion to making new genes
uz‐Zaman, M. H., & Ochman, H. (2026) · mBio · doi:10.1128/mbio.02016-26
One health perspectives on pharmaceutical and clinical effluents driving multidrug resistance in aquatic ecosystems: a comprehensive review
Tyagi, A., Rajput, M., & Mishra, S. (2026) · Frontiers in Systems Biology · doi:10.3389/fsysb.2026.1890380
Comparative genomic analysis of Agrobacterium salinitolerans provides insights into genetic diversity and pathogenic potential
Xiong, L., Cui, Y., Shi, Z., Yang, Y., Shen, X., Cai, Y., & Ji, X. (2026) · Archives of Microbiology · doi:10.1007/s00203-026-05256-z
Genome-based identification of hydrocarbon-metabolism-associated genes with putative relevance to polyethylene modification in Rhodococcus pyridinivorans AAa3
Elsayed, A. F., Youssef, H. I. A., Gebreel, H. M., Mahasneh, I., & Amin, D. H. (2026) · Gene · doi:10.1016/j.gene.2026.150460

Authors: Brockhurst, M. A., Harrison, E., Hall, J. P. J., Richards, T., McNally, A., & MacLean, C.
Affiliations: University of Sheffield (GB)
University of Liverpool (GB)
University of Exeter (GB)
University of Birmingham (GB)
Corresponding author: Brockhurst, Michael A.
ORCID: Brockhurst, Michael A.
Harrison, Ellie
Hall, James P.J.
Richards, Thomas
McNally, Alan
Venue: Current Biology
Publisher: Elsevier BV
Published: 2019-10
Volume: 29
Issue: 20
Pages: R1094-R1103
ISSN: 0960-9822 (ISSN-L)
DOI: 10.1016/j.cub.2019.08.012
OpenAlex: W2982249296
Cited by: 385
References: 131
Citations by year: 2026: 58 · 2025: 84 · 2024: 54 · 2023: 48 · 2022: 58 · 2021: 55 · 2020: 28
FWCI: 3.16
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 386 d)
Locations: Current Biology (publishedVersion)
PubMed (publishedVersion)
Research Explorer (The University of Manchester) (publishedVersion, other-oa)
White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
University of Birmingham Research Portal (University of Birmingham) (submittedVersion, cc-by-nc-nd)
University of Birmingham Research Portal (University of Birmingham) (submittedVersion, other-oa)
Funders: Natural Environment Research Council
Biotechnology and Biological Sciences Research Council
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords: pan-genome, accessory genome, core genome, horizontal gene transfer, gene loss, mobile genetic elements, prokaryotic genomes, eukaryotic genomes, gene content variation
MeSH terms: Biological Evolution, Phylogeny, Genome, Bacterial, Evolution, Molecular, Metagenome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The Ecology and Evolution of Pangenomes

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks