The Ecology and Evolution of Pangenomes

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 · see citing works

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 · see citing works

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 2,644 · see citing works

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 · see citing works

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 · see citing works

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 1,752 · see citing works

Effective population size and patterns of molecular evolution and variation

Charlesworth, B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2526 · Cited by 1,698 · see citing works

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 · see citing works

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 1,312 · see citing works

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 1,190 · see citing works

Genomic Islands in Pathogenic and Environmental Microorganisms

Dobrindt, U., Hochhut, B., Hentschel, U., & Hacker, J. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro884 · Cited by 1,188 · see citing works

Horizontal gene transfer among genomes: The complexity hypothesis

Jain, R., Rivera, M. C., & Lake, J. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.3801 · Cited by 1,170 · see citing works

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae

Rozwandowicz, M., Brouwer, M. S. M., Fischer, J., Wagenaar, J. A., González‐Zorn, B., Guerra, B., Mevius, D. J., & Hordijk, J. (2017) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkx488 · Cited by 1,027 · see citing works

Ecology drives a global network of gene exchange connecting the human microbiome

Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011) · Nature · doi:10.1038/nature10571 · Cited by 953 · see citing works

Deletional bias and the evolution of bacterial genomes.

Mira, A., Ochman, H., & Moran, N. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02447-7 · Cited by 850 · see citing works

Epidemiology and genetics in the coevolution of parasites and hosts

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Bacteriophage Host Range and Bacterial Resistance

Hyman, P., & Abedon, S. T. (2010) · Advances in applied microbiology · doi:10.1016/s0065-2164(10)70007-1 · Cited by 823 · see citing works

Host receptors for bacteriophage adsorption

Silva, J. B., Storms, Z. J., & Sauvageau, D. (2016) · FEMS Microbiology Letters · doi:10.1093/femsle/fnw002 · Cited by 787 · see citing works

Bacterial transformation: distribution, shared mechanisms and divergent control

Johnston, C., Martin, B., Fichant, G. A., Polard, P., & Claverys, J. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3199 · Cited by 737 · see citing works

Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments

Karkman, A., Pärnänen, K., & Larsson, D. G. J. (2019) · Nature Communications · doi:10.1038/s41467-018-07992-3 · Cited by 628 · see citing works

You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes

Doolittle, W. F. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(98)01494-2 · Cited by 600 · see citing works

Mutant phenotypes for thousands of bacterial genes of unknown function

Price, M. N., Wetmore, K. M., Waters, R. J., Callaghan, M., Ray, J., Liu, H., Kuehl, J. V., Melnyk, R. A., Lamson, J. S., Suh, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0124-0 · Cited by 576 · see citing works

Intercellular Nanotubes Mediate Bacterial Communication

Dubey, G. P., & Ben‐Yehuda, S. (2011) · Cell · doi:10.1016/j.cell.2011.01.015 · Cited by 567 · see citing works

Fitness Costs of Plasmids: a Limit to Plasmid Transmission

Millán, Á. S., & MacLean, R. C. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.mtbp-0016-2017 · Cited by 560 · see citing works

H-NS Mediates the Silencing of Laterally Acquired Genes in Bacteria

Lucchini, S., Rowley, G., Goldberg, M. D., Hurd, D., Harrison, M., & Hinton, J. C. D. (2006) · PLoS Pathogens · doi:10.1371/journal.ppat.0020081 · Cited by 557 · see citing works

Genomic evidence for two functionally distinct gene classes

Rivera, M. C., Jain, R., Moore, J. E., & Lake, J. A. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.11.6239 · Cited by 544 · see citing works

The multiplicity of domains in proteins.

Doolittle, R. (1995) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.64.070195.001443 · Cited by 540 · see citing works

Pan genome of the phytoplankton Emiliania underpins its global distribution

Emiliania huxleyi Annotation Consortium, Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., et al. (2013) · Nature · doi:10.1038/nature12221 · Cited by 516 · see citing works

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer

Pál, C., Papp, B., & Lercher, M. J. (2005) · Nature Genetics · doi:10.1038/ng1686 · Cited by 505 · see citing works

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

van Opijnen, T., & Camilli, A. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3033 · Cited by 495 · see citing works

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal <i>Enterobacteriaceae</i>

Stecher, B., Denzler, R., Maier, L., Bernet, F., Sanders, M. J., Pickard, D. J., Barthel, M., Westendorf, A. M., Krogfelt, K. A., Walker, A. W., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113246109 · Cited by 492 · see citing works

Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast

Heinemann, J. A., & Sprague, G. F. (1989) · Nature · doi:10.1038/340205a0 · Cited by 491 · see citing works

A global network of coexisting microbes from environmental and whole-genome sequence dataPreprint

Chaffron, S., Rehrauer, H., Pernthaler, J., & von Mering, C. (2010) · Genome Research · doi:10.1101/gr.104521.109 · Cited by 491 · see citing works

Biased biological functions of horizontally transferred genes in prokaryotic genomes

Nakamura, Y., Itoh, T., Matsuda, H., & Gojobori, T. (2004) · Nature Genetics · doi:10.1038/ng1381 · Cited by 480 · see citing works

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

Coleman, J. J., Rounsley, S., Rodriguez-Carres, M., Kuo, A., Wasmann, C. C., Grimwood, J., Schmutz, J., Taga, M., White, G. J., Zhou, S., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000618 · Cited by 468 · see citing works

The SOS Response Controls Integron Recombination

Guérin, É., Cambray, G., Sanchez-Alberola, N., Campoy, S., Erill, I., Re, S. D., González‐Zorn, B., Barbé, J., Ploy, M.-C., & Mazel, D. (2009) · Science · doi:10.1126/science.1172914 · Cited by 463 · see citing works

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

Klümper, U., Riber, L., Dechesne, A., Sannazzaro, A. I., Hansen, L. H., Sørensen, S. J., & Smets, B. F. (2014) · The ISME Journal · doi:10.1038/ismej.2014.191 · Cited by 460 · see citing works

The genetic basis of the fitness costs of antimicrobial resistance: a meta‐analysis approach

Vogwill, T., & MacLean, R. C. (2014) · Evolutionary Applications · doi:10.1111/eva.12202 · Cited by 444 · see citing works

Multidrug-Resistant Enterococci Lack CRISPR- cas

Palmer, K. L., & Gilmore, M. S. (2010) · mBio · doi:10.1128/mbio.00227-10 · Cited by 441 · see citing works

Microbial interactions lead to rapid micro-scale successions on model marine particles

Datta, M. S., Śliwerska, E., Gore, J., Polz, M. F., & Cordero, O. X. (2016) · Nature Communications · doi:10.1038/ncomms11965 · Cited by 429 · see citing works

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

Sorek, R., Zhu, Y., Creevey, C. J., Francino, M. P., Peer Bork, B., & Rubin, E. M. (2007) · Science · doi:10.1126/science.1147112 · Cited by 414 · see citing works

THE GENETICS OF HYPHAL FUSION AND VEGETATIVE INCOMPATIBILITY IN FILAMENTOUS ASCOMYCETE FUNGI

Glass, N. L., Jacobson, D. J., & Shiu, P. (2000) · Annual Review of Genetics · doi:10.1146/annurev.genet.34.1.165 · Cited by 414 · see citing works

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G., & Hanage, W. P. (2009) · Science · doi:10.1126/science.1159388 · Cited by 410 · see citing works

Why prokaryotes have pangenomes

McInerney, J. O., McNally, A., & O’Connell, M. J. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.40 · Cited by 403 · see citing works

Exploring the costs of horizontal gene transfer

Baltrus, D. A. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.04.002 · Cited by 398 · see citing works

Pervasive domestication of defective prophages by bacteria

Bobay, L., Touchon, M., & Rocha, E. P. C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405336111 · Cited by 387 · see citing works

Plasmid-mediated horizontal gene transfer is a coevolutionary process

Harrison, E., & Brockhurst, M. A. (2012) · Trends in Microbiology · doi:10.1016/j.tim.2012.04.003 · Cited by 366 · see citing works

Persistence and reversal of plasmid-mediated antibiotic resistance

Lopatkin, A. J., Meredith, H. R., Srimani, J. K., Pfeiffer, C., Durrett, R., & You, L. (2017) · Nature Communications · doi:10.1038/s41467-017-01532-1 · Cited by 364 · see citing works

Explaining microbial genomic diversity in light of evolutionary ecology

Cordero, O. X., & Polz, M. F. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3218 · Cited by 344 · see citing works

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

Nanda, A. M., Thormann, K. M., & Frunzke, J. (2014) · Journal of Bacteriology · doi:10.1128/jb.02230-14 · Cited by 319 · see citing works

Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation

Baharoglu, Z., Bikard, D., & Mazel, D. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001165 · Cited by 319 · see citing works

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene bla KPC

Sheppard, A. E., Stoesser, N. E., Wilson, D. J., Sebra, R., Kasarskis, A., Anson, L. W., Giess, A. P., Pankhurst, L. J., Vaughan, A., Grim, C. J., et al. (2016) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00464-16 · Cited by 298 · see citing works

Antibiotics as a selective driver for conjugation dynamics

Lopatkin, A. J., Huang, S., Smith, R. P., Srimani, J. K., Sysoeva, T. A., Bewick, S. A., Karig, D., & You, L. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.44 · Cited by 289 · see citing works

CRISPR-Cas and restriction–modification systems are compatible and increase phage resistance

Dupuis, M.-È., Villion, M., Magadán, A. H., & Moineau, S. (2013) · Nature Communications · doi:10.1038/ncomms3087 · Cited by 286 · see citing works

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

Goldberg, G. W., Jiang, W., Bikard, D., & Marraffini, L. A. (2014) · Nature · doi:10.1038/nature13637 · Cited by 284 · see citing works

Genomic-scale exchange of mRNA between a parasitic plant and its hosts

Kim, G., LeBlanc, M. L., Wafula, E. K., dePamphilis, C. W., & Westwood, J. H. (2014) · Science · doi:10.1126/science.1253122 · Cited by 284 · see citing works

Gene Transfer Potential of Outer Membrane Vesicles of Acinetobacter baylyi and Effects of Stress on Vesiculation

Fulsundar, S., Harms, K., Flaten, G. E., Johnsen, P. J., Chopade, B. A., & Nielsen, K. M. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.04248-13 · Cited by 267 · see citing works

Network analyses structure genetic diversity in independent genetic worlds

Halary, S., Leigh, J., Cheaib, B. A., Lopez, P., & Bapteste, E. P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908978107 · Cited by 263 · see citing works

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

Faure, G., Shmakov, S., Yan, W. X., Cheng, D. R., Scott, D. A., Peters, J. E., Makarova, K. S., & Koonin, E. V. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0204-7 · Cited by 262 · see citing works

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

Millán, Á. S., Peña‐Miller, R., Toll‐Riera, M., Halbert, Z. V., McLean, A. R., Cooper, B. S., & MacLean, R. C. (2014) · Nature Communications · doi:10.1038/ncomms6208 · Cited by 259 · see citing works

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

Harrison, E., Guymer, D., Spiers, A. J., Paterson, S., & Brockhurst, M. A. (2015) · Current Biology · doi:10.1016/j.cub.2015.06.024 · Cited by 256 · see citing works

Trends and barriers to lateral gene transfer in prokaryotes

Popa, O., & Dagan, T. (2011) · Current Opinion in Microbiology · doi:10.1016/j.mib.2011.07.027 · Cited by 251 · see citing works

Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts

Porse, A., Schønning, K., Munck, C., & Sommer, M. O. A. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw163 · Cited by 237 · see citing works

Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life

Gil, R., Sabater‐Muñoz, B., Latorre, A., Silva, F. J., & Moyá, A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.062067299 · Cited by 227 · see citing works

Complete sequence of the IncP‐9 TOL plasmid pWW0 from Pseudomonas putida

Greated, A., Lambertsen, L. M., Williams, P. A., & Thomas, C. M. (2002) · Environmental Microbiology · doi:10.1046/j.1462-2920.2002.00305.x · Cited by 217 · see citing works

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

Cohen, O., Gophna, U., & Pupko, T. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq333 · Cited by 194 · see citing works

Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

Loftie‐Eaton, W., Bashford, K., Quinn, H., Dong, K., Millstein, J., Hunter, S. S., Thomason, M. K., Merrikh, H., Ponciano, J. M., & Top, E. M. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0243-2 · Cited by 191 · see citing works

DNA-uptake machinery of naturally competent Vibrio cholerae

Seitz, P., & Blokesch, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1315647110 · Cited by 190 · see citing works

Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa

Millán, Á. S., Toll‐Riera, M., Qi, Q., & MacLean, R. C. (2015) · Nature Communications · doi:10.1038/ncomms7845 · Cited by 187 · see citing works

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

Hall, J. P. J., Wood, A. J., Harrison, E., & Brockhurst, M. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600974113 · Cited by 186 · see citing works

The fate of laterally transferred genes: Life in the fast lane to adaptation or deathPreprint

Hao, W., & Golding, G. B. (2006) · Genome Research · doi:10.1101/gr.4746406 · Cited by 184 · see citing works

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virusPreprint

Monier, A., Pagarete, A., de Vargas, C., Allen, M. J., Read, B. A., Claverie, J., & Ogata, H. (2009) · Genome Research · doi:10.1101/gr.091686.109 · Cited by 183 · see citing works

Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell

Makarova, K. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki775 · Cited by 181 · see citing works

Natural competence for transformation

Blokesch, M. (2016) · Current Biology · doi:10.1016/j.cub.2016.08.058 · Cited by 176 · see citing works

Adaptation as organism design

Gardner, A. (2009) · Biology Letters · doi:10.1098/rsbl.2009.0674 · Cited by 173 · see citing works

Theory of prokaryotic genome evolution

Sela, I., Wolf, Y. I., & Koonin, E. V. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614083113 · Cited by 166 · see citing works

Regulation of genetic flux between bacteria by restriction–modification systems

Oliveira, P. H., Touchon, M., & Rocha, E. P. C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603257113 · Cited by 166 · see citing works

Parallel independent evolution of pathogenicity within the genus Yersinia

Reuter, S., Connor, T. R., Barquist, L., Walker, D., Feltwell, T., Harris, S. R., Fookes, M. C., Hall, M., Petty, N. K., Fuchs, T. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317161111 · Cited by 165 · see citing works

DNA Sequence Similarity Requirements for Interspecific Recombination in Bacillus

Majewski, J., & Cohan, F. M. (1999) · Genetics · doi:10.1093/genetics/153.4.1525 · Cited by 164 · see citing works

Social behavior and decision making in bacterial conjugation

Koraimann, G., & Wagner, M. A. (2014) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2014.00054 · Cited by 163 · see citing works

Broad host range plasmids

Jain, A. Y., & Srivastava, P. (2013) · FEMS Microbiology Letters · doi:10.1111/1574-6968.12241 · Cited by 162 · see citing works

Horizontal Gene Transfer in Eukaryotic Plant Pathogens

Soanes, D. M., & Richards, T. A. (2014) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-102313-050127 · Cited by 159 · see citing works

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

Kloesges, T., Popa, O., Martin, W. F., & Dagan, T. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq297 · Cited by 158 · see citing works

Crossing Over Between Regions of Limited Homology in Escherichia coli: RecA-Dependent and RecA-Independent Pathways

Lovett, S. T., Hurley, R. L., Sutera, V. A., Aubuchon, R. H., & Lebedeva, M. A. (2002) · Genetics · doi:10.1093/genetics/160.3.851 · Cited by 155 · see citing works

Factors driving effective population size and pan-genome evolution in bacteria

Bobay, L., & Ochman, H. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1272-4 · Cited by 150 · see citing works

Migration and horizontal gene transfer divide microbial genomes into multiple niches

Niehus, R., Mitri, S., Fletcher, A. G., & Foster, K. R. (2015) · Nature Communications · doi:10.1038/ncomms9924 · Cited by 150 · see citing works

Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

Vos, M., Hesselman, M. C., Beek, T. A. H. T., van Passel, M. W. J., & Eyre‐Walker, A. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.07.006 · Cited by 147 · see citing works

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution

McNally, A., Thomson, N. R., Reuter, S., & Wren, B. W. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2015.29 · Cited by 145 · see citing works

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

Baumdicker, F., Hess, W. R., & Pfaffelhuber, P. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs016 · Cited by 144 · see citing works

Transfer of a Supernumerary Chromosome Between Vegetatively Incompatible Biotypes of the Fungus Colletotrichum gloeosporioides

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CRISPR-Cas-Mediated Phage Resistance Enhances Horizontal Gene Transfer by Transduction

Watson, B. N. J., Staals, R. H. J., & Fineran, P. C. (2018) · mBio · doi:10.1128/mbio.02406-17 · Cited by 140 · see citing works

Too Much Eukaryote LGT

Martin, W. F. (2017) · BioEssays · doi:10.1002/bies.201700115 · Cited by 136 · see citing works

Association between translation efficiency and horizontal gene transfer within microbial communities

Tuller, T., Girshovich, Y., Sella, Y., Kreimer, A., Freilich, S., Kupiec, M., Gophna, U., & Ruppin, E. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr054 · Cited by 129 · see citing works

Pan-genome analyses of model fungal species

McCarthy, C. G. P., & Fitzpatrick, D. A. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000243 · Cited by 122 · see citing works

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales

Gophna, U., Kristensen, D. M., Wolf, Y. I., Popa, O., Drevet, C., & Koonin, E. V. (2015) · The ISME Journal · doi:10.1038/ismej.2015.20 · Cited by 119 · see citing works

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

Collins, R. E., & Higgs, P. G. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss163 · Cited by 116 · see citing works

Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations

Fox, R., Zhong, X., Krone, S. M., & Top, E. M. (2008) · The ISME Journal · doi:10.1038/ismej.2008.53 · Cited by 115 · see citing works

Gene mobility promotes the spread of resistance in bacterial populations

Stevenson, C., Hall, J. P. J., Harrison, E., Wood, A. J., & Brockhurst, M. A. (2017) · The ISME Journal · doi:10.1038/ismej.2017.42 · Cited by 112 · see citing works

Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics

Rocha, E. P. C. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy078 · Cited by 110 · see citing works

Prokaryote genome fluidity is dependent on effective population size

Andreani, N. A., Hesse, E., & Vos, M. (2017) · The ISME Journal · doi:10.1038/ismej.2017.36 · Cited by 103 · see citing works

Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress

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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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Genic Selection Within Prokaryotic Pangenomes

Douglas, G. M., & Shapiro, B. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab234 · Cited by 27 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 25 · see citing works

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 · see citing works

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 25 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 22 · see citing works

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 · see citing works

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 21 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 21 · see citing works

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 16 · see citing works

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 19 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Pangenomes and Selection: The Public Goods Hypothesis

McInerney, J. O., Whelan, F., Domingo-Sananes, M. R., McNally, A., & O’Connell, M. J. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0_7 · Cited by 20 · see citing works

Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes

Baumdicker, F., & Kupczok, A. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad067 · Cited by 12 · see citing works

Why prokaryotes have pangenomes

McInerney, J. O., McNally, A., & O’Connell, M. J. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.40 · Cited by 403 · see citing works

Reply to ‘The population genetics of pangenomes’

McInerney, J. O., McNally, A., & O’Connell, M. J. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0068-4 · Cited by 11 · see citing works