Periodic Reporting for period 2 - XYL-EID (Determinants of Xylella fastidiosa host specificity)
Reporting period: 2018-10-01 to 2019-09-30
Despite its importance as a plant pathogen, there are no hypotheses on the determinants of X. fastidiosa host specificity. Because of its recent introduction in Europe, where host plants as well as the environment represent novel opportunities for expansion, it is of paramount importance to learn how X. fastidiosa adapts. This information could then be used in an attempt to limit its impact where it is already present, as well as its potential threat to risk areas where it could be disseminated. This project aims to address this very important knowledge gap, notably by studying the recent adaptation of this bacterium to olive trees in Southern Italy.
As recombination is believed to play a major role in X. fastidiosa’s host specificity, we then sought to determine whether we could link recombination patterns to a specific host plant species. However, by using a data set of 72 genomes belonging to different subspecies, no such correlation could be made (8).
We then chose to study a population with incipient host adaptation by focusing on the current disease epidemic in Apulia to identify loci involved in the early stages of host adaptation. By doing so, we hoped to identify loci under positive selection, hypothesizing that those are important for host adaptation and, ultimately, host specificity.
We sampled 74 twigs from X. fastidiosa infected olive trees from the beginning of the outbreak (2013) until 2017 across the affected area. The majority of the samples were first isolated before being sent for Illumina sequencing. Only a few single nucleotide polymorphisms (SNPs) were detected when comparing the whole-genome sequences of these isolates to the genome of the reference Apulian strain De Donno (9), further confirming that a single introduction is at the origin of this outbreak in Italy (unpublished data). Genomic comparison of these Apulian isolates with three Costa Rican ones corroborated that the strain present in Apulia originates from Central America. These genomic comparisons have enabled us to identify a few mutations that differentiate the Apulian isolates infecting olive trees from the Costa Rican one infecting coffee (unpublished results). The genes affected by these mutations are going to be further examined by reverse genetics in order to determine whether they are involved in X. fastidiosa adaptation to olive trees in Apulia. Moreover, we are currently looking at the presence of genes under positive selection in the Apulian data set.
We have presented the results of this project in several conferences, workshops and seminars, of which some where attended not only by researchers but also by stakeholders (among which farmers, agri-cooperatives, nurseries and the European Commission). For instance, I attended and presented my results (poster presentations) at the two European conferences on X. fastidiosa (2017 and 2019) organized notably by the European Food Safety Authority (EFSA).
I was also invited to give a talk at the Phytoma-España conference on X. fastidiosa in order to impart our knowledge on what we have learned so far from X. fastidiosa’s genomic analyses.
This is the first comprehensive study which aims at tackling the long-lasting question of the determinants of X. fastidiosa host specificity.
1. European Food Safety Authority (EFSA). Update of the Xylella spp. host plant database. EFSA Journal 16, (2018).
2. Serio, F. D. et al. Collection of data and information on biology and control of vectors of Xylella fastidiosa. EFSA Journal 102 (2019).
3. EFSA Panel on Plant Health (PLH) et al. Update of the Scientific Opinion on the risks to plant health posed by Xylella fastidiosa in the EU territory. EFSA Journal 200 (2019) doi:10.2903/j.efsa.2019.5665.
4. EFSA Panel on Plant Health (EFSA PLH Panel) et al. Updated pest categorisation of Xylella fastidiosa. EFSA Journal 16, (2018).
5. Marchi, G. et al. First detection of Xylella fastidiosa subsp. multiplex DNA in Tuscany (Italy). Phytopathologia Mediterranea 57, (2018).
6. Scally, M., Schuenzel, E. L., Stouthamer, R. & Nunney, L. Multilocus sequence type system for the plant pathogen Xylella fastidiosa and relative contributions of recombination and point mutation to clonal diversity. Applied and Environmental Microbiology 71, 8491–8499 (2005).
7. Sicard, A. et al. Xylella fastidiosa : Insights into an emerging plant pathogen. Annual Review of Phytopathology 56, (2018).
8. Vanhove, M. et al. Genomic diversity and recombination among Xylella fastidiosa subspecies. Appl Environ Microbiol AEM.02972-18 aem;AEM.02972-18v1 (2019) doi:10.1128/AEM.02972-18.
9. Giampetruzzi, A. et al. Complete genome sequence of the olive-infecting strain Xylella fastidiosa subsp. pauca De Donno. Genome announcements 5, e00569–17 (2017).