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

Population genomics of Klebsiella pneumoniae
Wyres, K. L., Lam, M. M. C., & Holt, K. E. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0315-1 · Cited by 1,175
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Gautreau, G., Bazin, A., Gachet, M., Planel, R., Burlot, L., Dubois, M., Perrin, A., Médigue, C., Calteau, A., Cruveiller, S., et al. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007732 · Cited by 293
The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution
Botelho, J., & Schulenburg, H. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2020.05.011 · Cited by 238
Plant NLR diversity: the known unknowns of pan-NLRomes
Barragan, A. C., & Weigel, D. (2020) · The Plant Cell · doi:10.1093/plcell/koaa002 · Cited by 213
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Khedkar, S., Smyshlyaev, G., Letunić, I., Maistrenko, O. M., Coelho, L. P., Orakov, A. N., Forslund, S. K., Hildebrand, F., Lütge, M., Schmidt, T., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac163 · Cited by 195
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
Ma, B., Lu, C., Wang, Y., Yu, J., Zhao, K., Xue, R., Ren, H., Lv, X., Pan, R., Zhang, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43000-z · Cited by 203
Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals
Sinha, D., Maurya, A. K., Abdi, G., Majeed, M., Agarwal, R., Mukherjee, R., Ganguly, S., Aziz, R., Bhatia, M., Majgaonkar, A., et al. (2023) · Genes · doi:10.3390/genes14071484 · Cited by 184
Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations
Haudiquet, M., de Sousa, J. A. M., Touchon, M., & Rocha, E. P. C. (2022) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2021.0234 · Cited by 156
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa
Wheatley, R. M., & MacLean, R. C. (2020) · The ISME Journal · doi:10.1038/s41396-020-00860-3 · Cited by 146
Genetic innovations in animal–microbe symbioses
Perreau, J. M., & Moran, N. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00395-z · Cited by 141
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
Maistrenko, O. M., Mende, D. R., Lütge, M., Hildebrand, F., Schmidt, T., Li, S. S., Rodrigues, J. F. M., von Mering, C., Coelho, L. P., Huerta‐Cepas, J., et al. (2020) · The ISME Journal · doi:10.1038/s41396-020-0600-z · Cited by 134
Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria
Shi, Y., Hirschmann, M., Shi, Y., Ahmed, S., Abebew, D., Tobias, N. J., Grün, P., Crames, J. J., Pöschel, L., Kuttenlochner, W., et al. (2022) · Nature Chemistry · doi:10.1038/s41557-022-00923-2 · Cited by 122
Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet
Sessitsch, A., Wakelin, S. A., Schloter, M., Maguin, E., Cernava, T., Champomier‐Vergès, M., Charles, T. C., Cotter, P. D., Ferrocino, I., Kriaa, A., et al. (2023) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00212-22 · Cited by 122
Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species
Ellegaard, K., Suenami, S., Miyazaki, R., & Engel, P. (2020) · Current Biology · doi:10.1016/j.cub.2020.04.070 · Cited by 112
Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes
Gluck‐Thaler, E., Ralston, T. I., Konkel, Z. M., Ocampos, C. J. G., Ganeshan, V. D., Dorrance, A. E., Niblack, T. L., Wood, C. W., Slot, J. C., Lopez-Nicora, H. D., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac109 · Cited by 113
Ecogenetics of antibiotic resistance in Listeria monocytogenes
Baquero, F., Lanza, V. F., Duval, M., & Coque, T. M. (2020) · Molecular Microbiology · doi:10.1111/mmi.14454 · Cited by 108
Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
Shaw, L. P., Chau, K., Kavanagh, J., AbuOun, M., Stubberfield, E. J., Gweon, H. S., Barker, L., Rodger, G., Bowes, M. J., Hubbard, A. T. M., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe3868 · Cited by 99
A host of armor: Prokaryotic immune strategies against mobile genetic elements
Mayo-Muñoz, D., Pinilla‐Redondo, R., Birkholz, N., & Fineran, P. C. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112672 · Cited by 103
The rise and fall of genes: origins and functions of plant pathogen pangenomes
Badet, T., & Croll, D. (2020) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2020.04.009 · Cited by 95
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes
Weigel, B. L., Miranda, K. K., Fogarty, E. C., Watson, A. R., & Pfister, C. A. (2022) · mSystems · doi:10.1128/msystems.01422-21 · Cited by 93
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design
Weilguny, L., Maio, N. D., Munro, R., Manser, C., Birney, E., Loose, M., & Goldman, N. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01580-z · Cited by 95
The Role of Gram-Negative Bacteria in Urinary Tract Infections: Current Concepts and Therapeutic Options
Behzadi, P., Urbán, E. Z., Matúz, M., Benkő, R., & Gajdács, M. (2020) · Advances in experimental medicine and biology · doi:10.1007/5584_2020_566 · Cited by 97
Current Techniques to Study Beneficial Plant-Microbe Interactions
Gamalero, E., Bona, E., & Glick, B. R. (2022) · Microorganisms · doi:10.3390/microorganisms10071380 · Cited by 80
Coinfinder: detecting significant associations and dissociations in pangenomes
Whelan, F. J., Rusilowicz, M., & McInerney, J. O. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000338 · Cited by 71
Mechanisms That Shape Microbial Pangenomes
Domingo-Sananes, M. R., & McInerney, J. O. (2021) · Trends in Microbiology · doi:10.1016/j.tim.2020.12.004 · Cited by 74
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.-M., He, B.-B., Cai, P., Zhong, Z., Feng, C., Neelakantan, P., et al. (2023) · Microbiome · doi:10.1186/s40168-023-01540-y · Cited by 72
“In RiPPs terms, other subtypes of BGCs and hybrid BGCs are clustered into “Others”. rSAM‑Modified RiPPs consist of RaS‑RiPP, ranthipeptide and sactipeptide enhancing niche adaptation or host fitness [27].”
Ecological dynamics of plasmid transfer and persistence in microbial communities
Bottery, M. J. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102152 · Cited by 72
Techniques in bacterial strain typing: past, present, and future
Simar, S. R., Hanson, B., & Arias, C. A. (2021) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0000000000000743 · Cited by 71
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Colquhoun, R., Hall, M. B., Lima, L., Roberts, L. W., Malone, K. M., Hunt, M., Letcher, B., Hawkey, J., George, S. A., Pankhurst, L. J., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02473-1 · Cited by 69
The Ingenuity of Bacterial Genomes
Kirchberger, P. C., Schmidt, M. L., & Ochman, H. (2020) · Annual Review of Microbiology · doi:10.1146/annurev-micro-020518-115822 · Cited by 68
Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA
Matuszewska, M., Murray, G. G. R., Ba, X., Wood, R. M., Holmes, M. A., & Weinert, L. A. (2022) · eLife · doi:10.7554/elife.74819 · Cited by 71
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) · Genome Medicine · doi:10.1186/s13073-021-00992-x · Cited by 65
Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition
Dimitriu, T., Kurilovich, E., Łapińska, U., Severinov, K., Pagliara, S., Szczelkun, M. D., & Westra, E. R. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.11.014 · Cited by 63
Robust analysis of prokaryotic pangenome gene gain and loss rates with PanstripePreprint
Tonkin‐Hill, G. Q., Gladstone, R. A., Pöntinen, A. K., Arredondo-Alonso, S., Bentley, S. D., & Corander, J. (2023) · Genome Research · doi:10.1101/gr.277340.122 · Cited by 61
Why do plasmids manipulate the expression of bacterial phenotypes?
Billane, K. C., Harrison, E., Cameron, D. D., & Brockhurst, M. A. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0461 · Cited by 62
Self-citation
Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi
Drott, M. T., Rush, T. A., Satterlee, T. R., Giannone, R. J., Abraham, P. E., Greco, C., Venkatesh, N., Skerker, J. M., Glass, N. L., Labbé, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021683118 · Cited by 55
Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity
Jurdzinski, K. T., Mehrshad, M., Delgado, L. F., Deng, Z., Bertilsson, S., & Andersson, A. F. (2023) · Science Advances · doi:10.1126/sciadv.adg2059 · Cited by 51
The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range
Coluzzi, C., & Rocha, E. P. C. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf060 · Cited by 58
The relevance of pedigrees in the conservation genomics era
Galla, S. J., Brown, L., Couch‐Lewis, Y., Cubrinovska, I., Eason, D., Gooley, R. M., Hamilton, J. A., Heath, J. A., Hauser, S. S., Latch, E. K., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16192 · Cited by 60
Bacterial lifestyle shapes pangenomes
Dewar, A. E., Hao, C., Belcher, L. J., Ghoul, M., & West, S. A. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2320170121 · Cited by 57
Toward a high-quality pan-genome landscape ofBacillus subtilisby removal of confounding strains
Wu, H., Wang, D., & Gao, F. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa013 · Cited by 49
Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways
Gabrielaitė, M., Johansen, H. K., Molin, S., Nielsen, F. C., & Marvig, R. L. (2020) · mBio · doi:10.1128/mbio.02359-20 · Cited by 52
Prokaryote pangenomes are dynamic entities
Cummins, E., Hall, R. J., McInerney, J. O., & McNally, A. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.01.005 · Cited by 47
Self-citation
Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa
Botelho, J., Tüeffers, L., Fuß, J., Buchholz, F., Utpatel, C., Klockgether, J., Niemann, S., Tümmler, B., & Schulenburg, H. (2023) · EBioMedicine · doi:10.1016/j.ebiom.2023.104532 · Cited by 49
Pangenomics reveals alternative environmental lifestyles among chlamydiae
Köstlbacher, S., Collingro, A., Halter, T., Schulz, F., Jungbluth, S. P., & Horn, M. (2021) · Nature Communications · doi:10.1038/s41467-021-24294-3 · Cited by 45
Defence systems and horizontal gene transfer in bacteria
Kogay, R., Wolf, Y. I., & Koonin, E. V. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16630 · Cited by 43
Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types
Cummins, E., Hall, R. J., Connor, C. H., McInerney, J. O., & McNally, A. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000903 · Cited by 41
Self-citation
Renaissance for Phage-Based Bacterial Control
Schwarz, C., Mathieu, J., Gomez, J. A. L., Yu, P., & Alvarez, P. J. J. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c06232 · Cited by 41
A spectrum of verticality across genes
Nagies, F. S. P., Brueckner, J., Tria, F. D. K., & Martin, W. F. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009200 · Cited by 40
Different evolutionary trends form the twilight zone of the bacterial pan-genome
Horesh, G., Taylor–Brown, A., McGimpsey, S., Lassalle, F., Corander, J., Heinz, E., & Thomson, N. R. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000670 · Cited by 41
Machine learning enables prediction of metabolic system evolution in bacteria
Konno, N., & Iwasaki, W. (2023) · Science Advances · doi:10.1126/sciadv.adc9130 · Cited by 39
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Dmitrijeva, M., Ruscheweyh, H., Feer, L., Li, K., Miravet‐Verde, S., Sintsova, A., Mende, D. R., Zeller, G., & Sunagawa, S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1004 · Cited by 44
Limited and Strain-Specific Transcriptional and Growth Responses to Acquisition of a Multidrug Resistance Plasmid in Genetically Diverse Escherichia coli Lineages
Dunn, S. J., Carrilero, L., Brockhurst, M. A., & McNally, A. (2021) · mSystems · doi:10.1128/msystems.00083-21 · Cited by 40
Self-citation
The extended mobility of plasmids
Garcillán-Barcia, M., de la Cruz, F., & Rocha, E. P. C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf652 · Cited by 44
Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements
Chibani, C. M., Roth, O., Liesegang, H., & Wendling, C. C. (2020) · BMC Genomics · doi:10.1186/s12864-020-6735-5 · Cited by 35
mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation
Buck, M., Mehrshad, M., & Bertilsson, S. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac060 · Cited by 39
LoVis4u: a locus visualization tool for comparative genomics and coverage profiles
Egorov, A. A., & Atkinson, G. C. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf009 · Cited by 38
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility
Hall, R. J., Whelan, F. J., Cummins, E. A., Connor, C., McNally, A., & McInerney, J. O. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000650 · Cited by 36
Self-citation
An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element
Ramsay, J. P., Bastholm, T. R., Verdonk, C. J., Tambalo, D. D., Sullivan, J. T., Harold, L. K., Panganiban, B. A., Colombi, E., Perry, B. J., Jowsey, W. J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1217 · Cited by 36
Progress and opportunities through use of genomics in animal production
Jones, H. E., & Wilson, P. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.06.014 · Cited by 42
Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen
Gill, J. L., Hedge, J., Wilson, D. J., & MacLean, R. C. (2021) · mBio · doi:10.1128/mbio.02168-21 · Cited by 33
Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements
Ares-Arroyo, M., Coluzzi, C., de Sousa, J. A. M., & Rocha, E. P. C. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002796 · Cited by 33
Interspecific competition can drive plasmid loss from a focal species in a microbial community
Sünderhauf, D., Klümper, U., Gaze, W. H., Westra, E. R., & van Houte, S. (2023) · The ISME Journal · doi:10.1038/s41396-023-01487-w · Cited by 32
Genomic diversity of genus Limosilactobacillus
Ksiezarek, M., Grosso, F., Ribeiro, T. G., & Peixe, L. M. S. V. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000847 · Cited by 31
CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes
Butiuc-Keul, A. L., Farkas, A., Carpa, R., & Iordache, D. (2021) · Microbial Physiology · doi:10.1159/000516643 · Cited by 31
The global population structure and beta-lactamase repertoire of the opportunistic pathogen Serratia marcescens
Matteoli, F. P., Pedrosa‐Silva, F., Silva, L. D., & Giachini, A. J. (2021) · Genomics · doi:10.1016/j.ygeno.2021.08.009 · Cited by 29
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
Williams, T., Davín, A. A., Szánthó, L. L., Stamatakis, A., Wahl, N. A., Woodcroft, B., Soo, R. M., Eme, L., Sheridan, P. O., Gubry-Rangin, C., et al. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae129 · Cited by 30
Genic Selection Within Prokaryotic Pangenomes
Douglas, G. M., & Shapiro, B. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab234 · Cited by 27
Horizontal gene transfer in yeasts
Gonçalves, P. M., & Gonçalves, C. (2022) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2022.101950 · Cited by 29
The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer
Hall, J. P. J., Harrison, E., Pärnänen, K. M. M., Virta, M., & Brockhurst, M. A. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01846 · Cited by 28
Self-citation
The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities
Kottara, A., Carrilero, L., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2021) · Microbiology · doi:10.1099/mic.0.001086 · Cited by 28
Self-citation
The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity
Jiao, J., Zhang, B., Li, M., Zhang, Z., & Tian, C. F. (2021) · The ISME Journal · doi:10.1038/s41396-021-01118-2 · Cited by 28
A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates
Pincus, N. B., Ozer, E. A., Allen, J. P., Nguyen, M., Davis, J. J., Winter, D. R., Chuang, C.-H., Chiu, C., Zamorano, L., Oliver, A., et al. (2020) · mBio · doi:10.1128/mbio.01527-20 · Cited by 26
Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi
Sezmis, A. L., Woods, L. C., Peleg, A. Y., & McDonald, M. J. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad028 · Cited by 26
Impact of key parameters involved with plant-microbe interaction in context to global climate change
Shree, B., Jayakrishnan, U., & Bhushan, S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1008451 · Cited by 27
Origins and evolution of biological novelty
Carscadden, K. A., Batstone, R. T., & Hauser, F. E. (2023) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12963 · Cited by 25
Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary originsPreprint
Vakirlis, N., & Kupczok, A. (2024) · Genome Research · doi:10.1101/gr.278977.124 · Cited by 24
Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of Genus Brevundimonas and Description of Brevundimonas pishanensis sp. nov.
Huang, Z., Yu, K., Xiao, Y., Wang, Y., Xiao, D., & Wang, D. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02468-21 · Cited by 24
Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification
Geng, R., Cheng, L., Cao, C., Liu, Z., Liu, D., Xiao, Z., Wu, X., Huang, Z., Feng, Q., Luo, C., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.854792 · Cited by 24
Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy
Jeffery, N. W., Lehnert, S. J., Kess, T., Layton, K. K. S., Wringe, B. F., & Stanley, R. R. E. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.886494 · Cited by 24
New Insights on Metabolic Features of Bacillus subtilis Based on Multistrain Genome-Scale Metabolic Modeling
Blázquez, B., León, D. S., Rojas, A., Tortajada, M., & Nogales, J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24087091 · Cited by 20
Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes
Carrilero, L., Kottara, A., Guymer, D., Harrison, E., Hall, J. P. J., & Brockhurst, M. A. (2021) · mBio · doi:10.1128/mbio.00558-21 · Cited by 23
Self-citation
Comprehensive and functional analyses reveal the genomic diversity and potential toxicity of Microcystis
Cao, H., Xu, D., Zhang, T., Ren, Q., Li, X., Ning, C., Zhang, Y., & Gao, R. (2022) · Harmful Algae · doi:10.1016/j.hal.2022.102186 · Cited by 23
A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation
Ceres, K., Stanhope, M. J., & Grohn, Y. T. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000839 · Cited by 23
Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems
Uceda-Campos, G., Feitosa-Junior, O. R., Santiago, C. R. N., Pierry, P. M., Zaini, P. A., de Santana, W. O., Martins, J., Barbosa, D., Digiampietri, L. A., Setúbal, J. C., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10050914 · Cited by 22
ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics
Zhang, Y., Zhang, H., Zhang, Z., Qian, Q., Zhang, Z., & Xiao, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac832 · Cited by 22
Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events
Kurushima, J., Campo, N., van Raaphorst, R., Cerckel, G., Polard, P., & Veening, J. (2020) · eLife · doi:10.7554/elife.58771 · Cited by 29
The proficiency of the original host species determines community-level plasmid dynamics
Kottara, A., Hall, J. P. J., & Brockhurst, M. A. (2021) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiab026 · Cited by 21
Self-citation
Diverse Populations of Staphylococcus pseudintermedius Colonize the Skin of Healthy Dogs
Fàbregas, N., Pérez, D., Viñes, J., Cuscó, A., Migura‐García, L., Ferrer, L., & Francino, O. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.03393-22 · Cited by 22
Assessment of assumptions underlying models of prokaryotic pangenome evolution
Sela, I., Wolf, Y. I., & Koonin, E. V. (2021) · BMC Biology · doi:10.1186/s12915-021-00960-2 · Cited by 20
Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome
McMullen, J. G., Bueno, E., Blow, F., & Douglas, A. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab127 · Cited by 18
The Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance
de Korne-Elenbaas, J., Bruisten, S. M., van Dam, A. P., Maiden, M. C. J., & Harrison, O. B. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02654-21 · Cited by 20
Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage
Raimondeau, P., Bianconi, M. E., Pereira, L., Parisod, C., Christin, P., & Dunning, L. T. (2023) · New Phytologist · doi:10.1111/nph.19272 · Cited by 20
Functional Genomic Analyses Reveal an Open Pan-genome for the Chloroviruses and a Potential for Genetic Innovation in New Isolates
Rodrigues, R. A. L., Queiroz, V. F., Ghosh, J. S., Dunigan, D. D., & Etten, J. L. V. (2021) · Journal of Virology · doi:10.1128/jvi.01367-21 · Cited by 19
Brucella ceti and Brucella pinnipedialis genome characterization unveils genetic features that highlight their zoonotic potential
Orsini, M., Ianni, A., & Zinzula, L. (2022) · MicrobiologyOpen · doi:10.1002/mbo3.1329 · Cited by 19
Biochemical and Genomic Characterization of Two New Strains of Lacticaseibacillus paracasei Isolated from the Traditional Corn-Based Beverage of South Africa, Mahewu, and Their Comparison with Strains Isolated from Kefir Grains
Moiseenko, K. V., Бегунова, А. В., Savinova, О. S., Glazunova, O. A., Рожкова, И. В., & Федорова, Т. В. (2023) · Foods · doi:10.3390/foods12010223 · Cited by 23
Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence
Ardern, Z., Chakraborty, S., Lenk, F., & Kaster, A. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad003 · Cited by 22
Transfer dynamics of antimicrobial resistance among gram-negative bacteria
Wang, B., Farhan, M. H. R., Yuan, L., Sui, Y., Chu, J., Yang, X., Li, Y., Huang, L., & Cheng, G. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.176347 · Cited by 18
Comparative Genomics of Shiga Toxin-Producing Escherichia coli Strains Isolated from Pediatric Patients with and without Hemolytic Uremic Syndrome from 2000 to 2016 in Finland
Bai, X.-N., Ylinen, E., Zhang, J., Salmenlinna, S., Halkilahti, J., Saxén, H., Narayanan, A., Jahnukainen, T., & Matussek, A. (2022) · Microbiology spectrum · doi:10.1128/spectrum.00660-22 · Cited by 22
Local adaptation, geographical distance and phylogenetic relatedness: Assessing the drivers of siderophore‐mediated social interactions in natural bacterial communities
Butaitė, E., Kramer, J., & Kümmerli, R. (2021) · Journal of Evolutionary Biology · doi:10.1111/jeb.13883 · Cited by 18

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