Diversity of Xanthomonas fragariae with MLVA & CRISPR

Smits, Theo H. M.; Pothier, Joël F.

Publication type:	Research data
Title:	Diversity of Xanthomonas fragariae with MLVA & CRISPR
Authors:	Smits, Theo H. M. Pothier, Joël F.
et. al:	No
Issue Date:	22-Apr-2018
Publisher / Ed. Institution:	European Nucleotide Archive
Language:	English
Subject (DDC):	572: Biochemistry 579: Microbiology
Abstract:	Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and Multiple-Locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described, and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed on discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study delivers typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.
URI:	https://www.ebi.ac.uk/ena/browser/view/PRJEB25730 https://digitalcollection.zhaw.ch/handle/11475/26245
Related publications:	https://doi.org/10.1099/mgen.0.000189
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Natural Resource Sciences (IUNR)
Published as part of the ZHAW project:	DROPSA – Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens
Appears in collections:	ZHAW Forschungsdaten Life Sciences and Facility Management

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Smits, T. H. M., & Pothier, J. F. (2018). Diversity of Xanthomonas fragariae with MLVA & CRISPR [Data set]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB25730

Smits, T.H.M. and Pothier, J.F. (2018) ‘Diversity of Xanthomonas fragariae with MLVA & CRISPR’. European Nucleotide Archive. Available at: https://www.ebi.ac.uk/ena/browser/view/PRJEB25730.

T. H. M. Smits and J. F. Pothier, “Diversity of Xanthomonas fragariae with MLVA & CRISPR.” European Nucleotide Archive, Apr. 22, 2018. [Online]. Available: https://www.ebi.ac.uk/ena/browser/view/PRJEB25730

SMITS, Theo H. M. und Joël F. POTHIER, 2018. Diversity of Xanthomonas fragariae with MLVA & CRISPR [online]. Data set. 22 April 2018. European Nucleotide Archive. Verfügbar unter: https://www.ebi.ac.uk/ena/browser/view/PRJEB25730

Smits, Theo H. M., and Joël F. Pothier. 2018. “Diversity of Xanthomonas Fragariae with MLVA & CRISPR.” Data set. European Nucleotide Archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB25730.

Smits, Theo H. M., and Joël F. Pothier. Diversity of Xanthomonas Fragariae with MLVA & CRISPR. European Nucleotide Archive, 22 Apr. 2018, https://www.ebi.ac.uk/ena/browser/view/PRJEB25730.