ena-STUDY-Zurich University of Applied Sciences (ZHAW), School of Life Sciences and Facility Management, Institute of Natural Resource Sciences-26-03-2018-15:19:10:004-895
Diversity of Xanthomonas fragariae with MLVA & CRISPR
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.
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.