Show simple item record

dc.contributor.authorGmiter, Dawid
dc.contributor.authorNawrot, Sylwia
dc.contributor.authorPacak, Ilona
dc.contributor.authorZegadło, Katarzyna
dc.contributor.authorKaca, Wiesław
dc.description.abstractThe bacterial pan-genome is a relatively new concept that refers to the number of genes observed in a given set of bacterial genome sequences, either at the intra- or inter-species level. Determining the pan-genome of a given species of bacteria using a large number of strains allows one to compare multiple genes and to determine evolutionary links between isolates. This information can help to determine population structure, diversity in terms of prevalence in a given environment and pathogenicity of microorganisms. Within this review, we explain the most important issues related to pan-genome studies. We also include a brief description of some selected bacterial pan-genomes. Finally, we propose an easy-toperform workflow to study bacterial pan-genomes that will facilitate nonexperts in a pan-genome-based investigation.en
dc.publisherWydawnictwo Uniwersytetu Łódzkiegopl
dc.relation.ispartofseriesActa Universitatis Lodziensis. Folia Biologica et Oecologicaen
dc.subjectbacterial pan-genomeen
dc.subjectgenome comparisonen
dc.subjectRoary workflowen
dc.titleTowards a better understanding of the bacterial pan-genomeen
dc.contributor.authorAffiliationGmiter, Dawid - Jan Kochanowski University of Kielce, Faculty of Natural Science, Institute of Biology, Division of Microbiology and Parasitology, Uniwersytecka 7, 25-460 Kielce, Polanden
dc.contributor.authorAffiliationNawrot, Sylwia - Jan Kochanowski University of Kielce, Faculty of Natural Science, Institute of Biology, Division of Microbiology and Parasitology, Uniwersytecka 7, 25-460 Kielce, Polanden
dc.contributor.authorAffiliationPacak, Ilona - Jan Kochanowski University of Kielce, Faculty of Natural Science, Institute of Biology, Division of Microbiology and Parasitology, Uniwersytecka 7, 25-460 Kielce, Polanden
dc.contributor.authorAffiliationZegadło, Katarzyna - Jan Kochanowski University of Kielce, Faculty of Natural Science, Institute of Biology, Division of Microbiology and Parasitology, Uniwersytecka 7, 25-460 Kielce, Polanden
dc.contributor.authorAffiliationKaca, Wiesław - Jan Kochanowski University of Kielce, Faculty of Natural Science, Institute of Biology, Division of Microbiology and Parasitology, Uniwersytecka 7, 25-460 Kielce, Polanden
dc.referencesAbudahab, K., Prada, J.M., Yang, Z., Bentley, S.D., Croucher, N.J., Corander, J., Aanensen, D.M. 2019. PANINI: pangenome neighbour identification for bacterial populations. Microbial Genomics, 5(4): e000220.en
dc.referencesArgemi, X., Matelska, D., Ginalski, K., Riegel, P., Hansmann, Y., Bloom, J., Pestel-Caron, M., Dahyot, S., Lebeurre, J., Prévost, G. 2018. Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. BMC Genomics, 19(1): 1–16.en
dc.referencesBazinet, A.L. 2017. Pan-genome and phylogeny of Bacillus cereus sensu lato. BMC Evolutionary Biology, 17(1): 1–16.en
dc.referencesBrynildsrud, O., Bohlin, J., Scheffer, L., Eldholm, V. 2016. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biology, 17(1): 1–9.en
dc.referencesCaierão, J., Paiva, J.A.C.D., Sampaio, J.L.M., da Silva, M.G., Santos, D.R. de S., Coelho, F.S., Fonseca, L. de S., Duarte, R.S., Armstrong, D.T., Regua-Mangia, A.H. 2016. Multilocus enzyme electrophoresis analysis of rapidly-growing mycobacteria: An alternative tool for identification and typing. International Journal of Infectious Diseases, 42: 11–16.en
dc.referencesCosta, S.S., Guimarães, L.C., Silva, A., Soares, S.C., Baraúna, R.A. 2020. First steps in the analysis of prokaryotic pan-genomes. Bioinformatics and Biology Insights, 14: 1–9.en
dc.referencesDecano, A.G., Downing, T. 2019. An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates. Scientific Reports, 9(1): 1–13.en
dc.referencesEspadinha, D., Sobral, R.G., Mendes, C.I., Méric, G., Sheppard, S.K., Carriço, J.A., Lencastre, H. de, Miragaia, M. 2019. Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages. Frontiers in Microbiology, 10: 1971.en
dc.referencesFreschi, L., Vincent, A.T., Jeukens, J., Emond-Rheault, J.G., Kukavica-Ibrulj, I., Dupont, M.J., Charette, S.J., Boyle, B., Levesque, R.C. 2019. The Pseudomonas aeruginosa Pan-genome provides new insights on its population structure, horizontal gene transfer, and pathogenicity. Genome Biology and Evolution, 11(1): 109–120.en
dc.referencesGordienko, E.N., Kazanov, M.D., Gelfand, M.S. 2013. Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica. Journal of Bacteriology, 195(12): 2786–2792.en
dc.referencesGrüning, B., Dale, R., Sjödin, A., Chapman, B.A., Rowe, J., Tomkins-Tinch, C.H., Köster, J., The Bioconda Team. 2018. Bioconda : sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15: 475–476.en
dc.referencesGuimarães, L.C., Benevides De Jesus, L., Vinícius, M., Viana, C., Silva, A., Thiago, R., Ramos, J., De, S., Soares, C., Azevedo, V. 2015. Inside the pan-genome – methods and software overview. Current Genomics, 16: 245–252.en
dc.referencesGuindon, S., Dufayard, J., Lefort, V., Anisimova, M., Hordijk, W., Gascuel, O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies assessing the performance of PhyML 3.0. Systematic Biology, 59(3): 307–321.en
dc.referencesGuo, Y., Song, G., Sun, M., Wang, J., Wang, Y. 2020. Prevalence and therapies of antibiotic-resistance in Staphylococcus aureus. Frontiers in Cellular and Infection Microbiology, 10: 107.en
dc.referencesHadfield, J., Croucher, N.J., Goater, R.J., Abudahab, K., Aanensen, D.M., Harris, S.R. 2018. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics, 34(2): 292–293.en
dc.referencesJamrozy, D.M., Harris, S.R., Mohamed, N., Peacock, S.J., Tan, C.Y., Parkhill, J., Anderson, A.S., Holden, M.T.G. 2016. Pangenomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic. Microbial Genomics, 2(5): e000058.en
dc.referencesJin, Y., Zhou, J., Zhou, J., Hu, M., Zhang, Q., Kong, N., Ren, H., Liang, L., Yue, J. 2020. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biology Direct, 15(1): 1–14.en
dc.referencesJohn, J., George, S., Nori, S.R.C., Nelson-Sathi, S., Pisani, D. 2019. Phylogenomic analysis reveals the evolutionary route of resistant genes in Staphylococcus aureus. Genome Biology and Evolution, 11(10): 2917–2926.en
dc.referencesLee, A.H.Y., Flibotte, S., Sinha, S., Paiero, A., Ehrlich, R.L., Balashov, S., Ehrlich, G.D., Zlosnik, J.E.A., Mell, J.C., Nislow, C. 2017. Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs. Genome Research, 27(4): 650–662.en
dc.referencesLloyd, J.P.B. 2018. Ubuntu on Windows for computational biology. protocols.Io. Available from: (accessed 28.06.2021).en
dc.referencesMahenthiralingam, E., Baldwin, A., Dowson, C.G. 2008. Burkholderia cepacia complex bacteria: Opportunistic pathogens with important natural biology. Journal of Applied Microbiology, 104(6): 1539–1551.en
dc.referencesMéric, G., Miragaia, M., De Been, M., Yahara, K., Pascoe, B., Mageiros, L., Mikhail, J., Harris, L. G., Wilkinson, T.S., Rolo, J., Lamble, S., Bray, J.E., Jolley, K.A., Hanage, W.P., Bowden, R., Maiden, M.C.J., Mack, D., De Lencastre, H., Feil, E.J., Corander J., Sheppard, S.K. 2015. Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biology and Evolution, 7(5): 1313–1328.en
dc.referencesMira, A., Martín-Cuadrado, A.B., D’Auria, G., Rodríguez-Valera, F. 2010. The bacterial pangenome: A new paradigm in microbiology. International Microbiology, 13(2): 45–57.en
dc.referencesMöller, S., Krabbenhöft, H.N., Tille, A., Paleino, D., Williams, A., Wolstencroft, K., Goble, C., Holland, R., Belhachemi, D., Plessy, C. 2010. Community-driven computational biology with Debian Linux. BMC Bioinformatics, 11(SUPPL. 12): S5.en
dc.referencesMosquera-Rendón, J., Rada-Bravo, A.M., Cárdenas-Brito, S., Corredor, M., Restrepo-Pineda, E., Benítez-Páez, A. 2016. Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species. BMC Genomics, 17(1): 1–15.en
dc.referencesPage, A.J., Cummins, C.A., Hunt, M., Wong, V.K., Reuter, S., Holden, M.T.G., Fookes, M., Falush, D., Keane, J.A., Parkhill, J. 2015. Roary: rapid large-scale prokaryote pangenome analysis. Bioinformatics, 31(22): 3691–3693.en
dc.referencesRambaut A. 2013. FigTree. Available from: (accessed 28.06.2021).en
dc.referencesRouli, L., Merhej, V., Fournier, P.E., Raoult, D. 2015. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes and New Infections, 7: 72–85.en
dc.referencesSeemann, T. 2014. Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30(14): 2068–2069.en
dc.referencesSitto, F., Battistuzzi, F.U. 2020. Estimating pangenomes with Roary. Molecular Biology and Evolution, 37(3): 933–939.en
dc.referencesThorpe, H.A., Bayliss, S.C., Sheppard, S.K., Feil, E.J. 2018. Piggy: A rapid, large-scale pangenome analysis tool for intergenic regions in bacteria. GigaScience, 7(4): 1–11.en
dc.referencesTouchon, M., Perrin, A., De Sousa, J.A.M., Vangchhia, B., Burn, S., O’Brien, C.L., Denamur, E., Gordon, D., Rocha, E.P.C. 2020. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genetics, 16(6): e1008866.en
dc.referencesWhelan, F.J., Rusilowicz, M., McInerney, J.O. 2020. Coinfinder: Detecting significant associations and dissociations in pangenomes. Microbial Genomics, 6(3): 1–7.en
dc.referencesZhou, J., Ren, H., Hu, M., Zhou, J., Li, B., Kong, N., Zhang, Q., Jin, Y., Liang, L., Yue, J. 2020. Characterization of Burkholderia cepacia complex core genome and the underlying recombination and positive selection. Frontiers in Genetics, 11: 1–15.en
dc.contributor.authorEmailGmiter, Dawid -
dc.contributor.authorEmailNawrot, Sylwia -
dc.contributor.authorEmailPacak, Ilona -
dc.contributor.authorEmailZegadło, Katarzyna -
dc.contributor.authorEmailKaca, Wiesław -

Files in this item


This item appears in the following Collection(s)

Show simple item record
Except where otherwise noted, this item's license is described as