Pokaż uproszczony rekord

The characterization of genome sequences diversity of Pseudomonas aeruginosa strains from international reference panel using wide range of in silico techniques

dc.contributor.authorPetruńko, Leon
dc.contributor.authorMusiał, Klaudia
dc.contributor.authorGmiter, Dawid
dc.date.accessioned2024-09-24T10:27:58Z
dc.date.available2024-09-24T10:27:58Z
dc.date.issued2024-09-18
dc.identifier.issn1730-2366
dc.identifier.urihttp://hdl.handle.net/11089/53226
dc.description.abstractPseudomonas aeruginosa is an important pathogen in patients suffering from Cystic Fibrosis as well as acute opportunistic infections in people without it. For the reason of P. aeruginosa having a broad range of habitats it’s diversity and adaptability lead it to be a very diverse species. Previous attempts of classifying P. aeruginosa strains based on their biochemical and genetic characteristics were made. In presented studied we performed additional characteristic of P. aeruginosa panel strains genomes using wide range of in silico approaches, including Single Nucleotide Polymorphisms (SNPs) - based phylogeny, as well as pan-genome and Intergenic Regions (IGRs) investigation. We shed light on strains diversity, expanding our knowledge about the strains assembled in this international panel. The results of our study may become the basis for further research aimed at fully understanding the pathogenesis of P. aeruginosa.en
dc.language.isoen
dc.publisherWydawnictwo Uniwersytetu Łódzkiegopl
dc.relation.ispartofseriesActa Universitatis Lodziensis. Folia Biologica et Oecologicaen
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0
dc.subjectPseudomonas aeruginosaen
dc.subjectreference panelen
dc.subjectpan-genomeen
dc.subjectintergenic regions (IGRs)en
dc.titleThe characterization of genome sequences diversity of Pseudomonas aeruginosa strains from international reference panel using wide range of in silico techniquesen
dc.typeArticle
dc.page.number72-84
dc.contributor.authorAffiliationPetruńko, Leon - Jan Kochanowski University of Kielce, Faculty of Natural Sciences, Institute of Biology, Department of Microbiology, Polanden
dc.contributor.authorAffiliationMusiał, Klaudia - Jan Kochanowski University of Kielce, Faculty of Natural Sciences, Institute of Biology, Department of Microbiology, Polanden
dc.contributor.authorAffiliationGmiter, Dawid - Jan Kochanowski University of Kielce, Faculty of Natural Sciences, Institute of Biology, Department of Microbiology, Polanden
dc.identifier.eissn2083-8484
dc.referencesBertels, F., Silander, O.K., Pachkov, M., Rainey, P. B., Van Nimwegen, E. 2014. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Molecular Biology and Evolution, 31(5).en
dc.referencesCroucher, N.J., Page, A.J., Connor, T.R., Delaney, A.J., Keane, J.A., Bentley, S.D., Parkhill, J., Harris, S.R. 2015. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research, 43(3), e15.en
dc.referencesCullen, L., Weiser, R., Olszak, T., Maldonado, R.F., Slachmuylders, L., Brackman, G., Paunova-Krasteva, T.S., Zarnowiec, P., Czerwonka, G., Reilly, J., Drevinek, P., Kaca, W., Melter, O., De Soyza, A., Perry, A., Winstanley, C., Stoitsova, S.R., Lavigne, R., Mahenthiralingam, E., Sá-Correia, I., Coenye, T., Drulis-Kawa, Z., Augustyniak, D., Valvano, M.A., McClean, S. 2015. Phenotypic characterization of an international Pseudomonas aeruginosa reference panel: strains of cystic fibrosis (CF) origin show less in vivo virulence than non-CF strains. Microbiology, 161(10), 1961–1977.en
dc.referencesDe Soyza, A., Hall, A.J., Mahenthiralingam, E., Drevinek, P., Kaca, W., Drulis-Kawa, Z., Stoitsova, S.R., Toth, V., Coenye, T., Zlosnik, J.E.A., Burns, J. L., Sá-Correia, I., De Vos, D., Pirnay, J.P., Kidd, T.J., Reid, D., Manos, J., Klockgether, J., Wiehlmann, L., Tümmler, B., McClean, S., Winstanley, C. 2013. Developing an international Pseudomonas aeruginosa reference panel. MicrobiologyOpen, 2(6).en
dc.referencesFreschi, L., Bertelli, C., Jeukens, J., Moore, M.P., Kukavica-Ibrulj, I., Emond-Rheault, J.G., Hamel, J., Fothergill, J.L., Tucker, N.P., McClean, S., Klockgether, J., De Soyza, A., Brinkman, F.S.L., Levesque, R.C., Winstanley, C. 2018. Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools. FEMS Microbiology Letters, 365(14).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.referencesGmiter, D., Nawrot, S., Pacak, I., Zegadło, K., Kaca, W. 2021. Towards a better understanding of the bacterial pan-genome. Acta Universitatis Lodziensis. Folia Biologica et Oecologica, 17, 84–96.en
dc.referencesGouy, M., Guindon, S., Gascuel, O. 2010. Sea view version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution, 27(2), 221–224.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.referencesMatus-Garcia, M., Nijveen, H., Van Passel, M.W.J. 2012. Promoter propagation in prokaryotes. Nucleic Acids Res. 40, 10032–10040.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.referencesNielsen, F.D., Møller-Jensen, J., Jørgensen, M.G. 2023. Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae. Frontiers in Bioinformatics, 3.en
dc.referencesOren, Y., Smith, M.B., Johns, N.I., Kaplan Zeevi, M., Biran, D., Ron, E.Z., Corander, J., Wang, H.W., Alm, E.J., Pupko, T. 2014. Transfer of noncoding DNA drives regulatory rewiring in Bacteria. Proc. Natl. Acad. Sci. U. S. A. 111, 16112–16117.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 pan-genome analysis. Bioinformatics, 31(22), 3691–3693.en
dc.referencesPage, A.J., Taylor, B., Delaney, A.J., Soares, J., Seemann, T., Keane, J.A., Harris, S.R. 2016. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microbial Genomics, 2(4), e000056.en
dc.referencesRagan, M.A., Beiko, R.G. 2009. Lateral genetic transfer: Open issues. Philos. Trans. R. Soc. B Biol. Sci. 364, 2241–2251.en
dc.referencesRevell, L.J. 2012. Phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3(2), 217–223.en
dc.referencesScience, E., Zhong, C., Han, M., Yang, P., Chen, C., Yu, H., Wang, L., Ning, K. 2019. Comprehensive analysis reveals the evolution and pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities. mSystems, 4(5), 1–19.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 pan-genome analysis tool for intergenic regions in bacteria. GigaScience, 7(4), 1–11en
dc.contributor.authorEmailPetruńko, Leon - leonpetrunko@gmail.com
dc.contributor.authorEmailMusiał, Klaudia - musial.klaudia0805@gmail.com
dc.contributor.authorEmailGmiter, Dawid - leonpetrunko@gmail.com
dc.identifier.doi10.18778/1730-2366.18.11
dc.relation.volume18


Pliki tej pozycji

Thumbnail
Nazwa:
72-84_Petrunko_et_al..pdf
Rozmiar:
847.8KB
Format:
PDF
Oglądaj/Otwórz

Pozycja umieszczona jest w następujących kolekcjach

Pokaż uproszczony rekord

https://creativecommons.org/licenses/by-nc-nd/4.0
Poza zaznaczonymi wyjątkami, licencja tej pozycji opisana jest jako https://creativecommons.org/licenses/by-nc-nd/4.0