High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

Sabina Żołędowska , Agata Motyka-Pomagruk , Wojciech Śledź , Alessio Mengoni , Ewa Łojkowska

Abstract

Background: Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline. Results: The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland. Conclusions: We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.
Author Sabina Żołędowska (IFB)
Sabina Żołędowska,,
- Intercollegiate Faculty of Biotechnology UG
, Agata Motyka-Pomagruk (IFB)
Agata Motyka-Pomagruk,,
- Intercollegiate Faculty of Biotechnology UG
, Wojciech Śledź (IFB / IB / DBiotech)
Wojciech Śledź,,
- Department of Biotechnology
, Alessio Mengoni
Alessio Mengoni,,
-
, Ewa Łojkowska (IFB / IB / DBiotech)
Ewa Łojkowska,,
- Department of Biotechnology
Journal seriesBMC Genomics, ISSN , e-ISSN 1471-2164, (A 35 pkt)
Issue year2018
Vol19
Pages1-16
Publication size in sheets0.75
Keywords in EnglishBlackleg, Pectinolytic erwinias, pan-genome, comparative genomics, phages, bacterial evolution, genome plasticity
DOIDOI:10.1186/s12864-018-5140-9
URL https://doi.org/10.1186/s12864-018-5140-9
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)40
ScoreMinisterial score = 35.0, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, ArticleFromJournal
Publication indicators WoS Impact Factor: 2017 = 3.73 (2) - 2017=4.257 (5)
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