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Current projects of the research group for environmental genomics and systems biology

XhortOMICs: Diagnostic and epidemiological tools for the Xanthomonas hortorum species-level clade

Many members of the bacterial genus Xanthomonas are plant pathogenic bacteria causing a broad range of diseases on economically relevant crops. Despite its recent reappearance and increased prevalence in many countries, the research on X. hortorum, the causal agent of bacterial blight in many important horticultural and ornamental plant species, has been very limited until now. The overall aim of the SNF-funded project XhortOMICs is to fill this gap by investigating the genomic diversity of X. hortorum at sub-species level in order to improve the existing taxonomy, develop novel specific diagnostic methods and to study the molecular basis of host-specificity in the individual pathovars of the species.

Several collaborations with European and international researchers in the domains of bacterial identification, genomics, comparative genomics and phytosanitary aspects are planned, including practical training courses. This SNF project is part of the larger interdisciplinary network EuroXanth (COST Action CA16107; EU-funded programme 2017-2021), aiming at integrating science to develop sustainable strategies for plant disease management of Xanthomonadaceae in Europe. As part of EuroXanth, the EGSB group is leading the WG2 on pathogen biology.

Project partners: Université Lyon 1 (FR), INRA Angers (FR), Flanders research institute for agriculture, fisheries and food ILVO (BE), COST Action CA16110 EuroXanth partners.
Funding agency: SNF, Grant IZCOZ0_177064
Project duration: 2018-2021
More information: COST Action CA16107EuroXanthWG2


Comparison of genomes belonging to different P. syringae pathovars.

DROPSA is a 4-year project involving 26 partners from Europe, Asia, New Zealand and North America. It focuses on new and emerging threats to the fruit industry due to cherry fruit fly Drosophila suzukii, as well as the bacterial pathogens Pseudomonas syringae pv. actinidiae, Xanthomonas fragariae and X. arboricola pv. pruni. These pathogens are a major concern because neither eradication nor containment are possible; hence the development of targeted integrated pest management (IPM) is vital to minimize the economic impact on fruit production in the EU region.

The EGSB group is leading the WP3 on biology and epidemiology of bacterial diseases as well as the Task 3.2 “Pathogen source-tracking and evolutionary risks” and Task 3.5 “Pathogen interactions with insect pollinators and Drosophila suzukii”. For this purpose, we have developed on-site detection tools for the three bacterial pathogens using comparative genomics (Bühlmann et al., 2013; Gétaz et al., 2017; Ruinelli et al., 2017). We have also established source-tracking tools for the X. fragariae pathogen for genotyping isolates and determining inoculum reservoirs and invasion routes impacting disease outbreaks.

Project partners: 26 partners worldwide
Client: EU 7th Framework Programme, Grant 613678
Project duration: 2014-2017
More information: DROPSA website - Poster - Brochure - Video