# Complete genome sequence data of Xylella fastidiosa subspecies multiplex ST88 and ST89 indicate distinct introductions in France

Amandine Cunty, Jessica Dittmer, Déborah Merda, Bruno Legendre, Benoit Remenant, Yannick Blanchard, Sophie Cesbron, Marie-Agnès Jacques, Pascal Gentit, Anne-Laure Boutigny

► To cite this version:

Amandine Cunty, Jessica Dittmer, Déborah Merda, Bruno Legendre, Benoit Remenant, et al.. Complete genome sequence data of Xylella fastidiosa subspecies multiplex ST88 and ST89 indicate distinct introductions in France. Data in Brief, 2025, 61, pp.111816. 10.1016/j.dib.2025.111816. anses-05418638

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Data Article

# Complete genome sequence data of *Xylella fastidiosa* subspecies *multiplex* ST88 and ST89 indicate distinct introductions in France

<figure><img src="image_2.png" /></figure>

Amandine Cunty<sup>a,1</sup>, Jessica Dittmer<sup>b,1</sup>, Déborah Merda<sup>c</sup>, Bruno Legendre<sup>a</sup>, Benoit Remenant<sup>a</sup>, Yannick Blanchard<sup>d</sup>, Sophie Cesbron<sup>b</sup>, Marie-Agnès Jacques<sup>b</sup>, Pascal Gentit<sup>a</sup>, Anne-Laure Boutigny<sup>a,*</sup>

ARTICLE INFO

Article history:
Received 2 May 2025
Revised 13 June 2025
Accepted 16 June 2025
Available online 21 June 2025

Dataset link: *Xylella fastidiosa* ST89 genome
sequencing and assembly

Dataset link: *Xylella fastidiosa* ST88 genome
sequencing and assembly

Keywords:

Sequence type

Quarantine bacteria

Long and short reads

PacBio

Illumina

ABSTRACT

*Xylella fastidiosa* is a Gram-negative bacterium native to the Americas and classified as a priority pest under EU regulations. This xylem-limited plant pathogenic bacterium has a wide host range and is transmitted by insect vectors. Since 2013, *X. fastidiosa* has been identified in several European countries including Italy, France, Spain and Portugal, with different subspecies and sequence types (ST) detected. Since 2015, most strains identified in France are of the subspecies *multiplex*, specifically ST6 and ST7. Two new STs of *X. fastidiosa* subsp. *multiplex*, ST88 and ST89, were recently detected in the region Provence-Alpes-Côte d'Azur (PACA), and one strain of each ST has been isolated from infected plants. To investigate the phylogenetic relationships between the four STs present in France, a complete circular genome and a single-contig genome were assembled for the ST89 and ST88 strains, respectively, by combining PacBio and Illumina sequencing data. A phylogenomic analysis was performed to investigate the phylogenetic position and potential origin of

ARTICLE INFO

<footnote><sup>a</sup>ANSES, Plant Health Laboratory, BVO Unit, Angers, France</footnote>

<footnote><sup>b</sup>UMR 1345, University of Angers, Institut Agro, INRAE, IRHS, SFR Quasav, Angers, France</footnote>

<footnote><sup>c</sup>ANSES, Food Safety Laboratory, SPAAD Unit, Maisons-Alfort, France</footnote>

<footnote><sup>d</sup>ANSES, Ploufragan Laboratory, VGB Unit, Ploufragan, France</footnote>

<footnote>* Corresponding author.</footnote>

<footnote>E-mail address: anne-laure.boutigny@anses.fr (A.-L. Boutigny).</footnote>

<footnote n="1">¹ These authors contributed equally to this work.</footnote>
these new strains. This data article contributes to improve
our knowledge of the diversity and origin of X. *fastidiosa*
subsp. *multiplex* in France and Europe.

© 2025 Published by Elsevier Inc.

This is an open access article under the CC BY license

(http://creativecommons.org/licenses/by/4.0/)

<table><caption>Specifications Table</caption><tr><td>Subject</td><td>Microbiology</td></tr><tr><td>Specific subject area</td><td>Bacteriology, Fastidious bacteria, Genomics</td></tr><tr><td>Type of data</td><td>Table, Figure</td></tr><tr><td>Data collection</td><td>Genomic data, Raw, Analyzed, Filtered, Processed<br>Genomic DNA extraction: Wizard Genomic DNA Purification Kit (Promega) and QuickPick™ SML Plant DNA kit (Bio-Nobile)<br>Genome sequencing platforms: Illumina MiSeq and PacBio<br>Bioinformatic tools: Canu v2.1.1, Flye v2.8.1, Circlator v1.5.6, Polca from the MaSuRCa toolkit v4.0.9, CheckM v1.1.6, Bakta v1.5.1</td></tr><tr><td>Data source location</td><td>Plant Health Laboratory of ANSES, Angers, France<br>IRHS, Angers, France</td></tr><tr><td>Data accessibility</td><td>Repository name: NCBI (www.ncbi.nlm.nih.gov)<br>Data identification number: Bioprojects PRJNA1234384 and PRJNA1234386<br>Direct URL to data:<br>LSV 52.37:<br>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1234384<br>https://www.ncbi.nlm.nih.gov/biosample/SAMN47296926<br>https://www.ncbi.nlm.nih.gov/sra/SRX27952896<br>https://www.ncbi.nlm.nih.gov/sra/SRX27952897<br>https://www.ncbi.nlm.nih.gov/sra/SRX27952898<br>LSV 52.52:<br>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1234386<br>https://www.ncbi.nlm.nih.gov/biosample/SAMN47297024<br>https://www.ncbi.nlm.nih.gov/sra/SRX27953175<br>https://www.ncbi.nlm.nih.gov/sra/SRX27953176<br>https://www.ncbi.nlm.nih.gov/sra/SRX27953177<br>Instructions for accessing these data: The complete genome sequences of Xylella fastidiosa subsp. multiplex strains LSV52.37 (ST88) and LSV52.52 (ST89) are available in the National Centre for Biotechnology Information (NCBI) database (Bioproject PRJNA1234384, Biosample SAMN47296926 for LSV52.37 and Bioproject PRJNA1234386, Biosample SAMN47297024 for LSV52.52). The raw data are available under the following accession numbers: SRR32648475 to SRR32648477 for LSV52.37 and SRR32648754 to SRR32648756 for LSV52.52.</td></tr><tr><td>Related research article</td><td>A. Cunty, B. Legendre, P. de Jerphanion, C. Dousset, A. Forveille, S. Paillard, V. Olivier, Update of the Xylella fastidiosa outbreak in France: two new variants detected and a new region affected, Eur. J. Plant Pathol. 163 (2022) 505–510. 10.1007/s10658-022-02492-z.</td></tr></table>

# 1. Value of the Data

* Data report on the high-quality genome sequences of two strains of X. *fastidiosa* subsp. *multiplex* ST88 and ST89 isolated in France.

* The data extend genomic data available for European strains of X. *fastidiosa* subsp. *multiplex* and are valuable for comparative genomics.

* The data provide a better overview of the diversity and origin of X. *fastidiosa* subsp. *multiplex* in France and Europe.

* The data support the hypothesis of two distinct introductions from the USA to France for both ST88 and ST89, rather than both ST88 and ST89 having evolved from strains already present
in France. These results are in accordance with the MLST analysis previously performed on these two strains [1].

## 2. Background

Xylella fastidiosa is a Gram-negative, xylem-limited phytopathogenic bacterium with a broad host range, which causes significant epidemics and economic losses in the Americas and Europe [2]. Despite being native to the Americas [3], since 2013 X. fastidiosa has been identified in various plant species in European countries with a Mediterranean climate, such as Italy, France, Spain and Portugal, with different subspecies and sequence types (ST) detected [2,4]. These detections are the result of multiple independent introductions likely originating from the USA [4,5]. In France, the subspecies multiplex was first detected in 2015 in Corsica and in the region Provence-Alpes-Côte d'Azur (PACA) (ST6 and ST7) and in 2020 in the Occitanie region (ST6) [1,6]. Also in 2020, two new STs of X. fastidiosa subsp. multiplex were identified in the PACA region at two different locations and in different host plants: (i) ST88 was detected on Polygala myrtifolia, Hebe sp., Osteospermum ecklonis, Lavandula x intermedia, Coronilla glauca and Euryops chrysanthe-moides and (ii) ST89 was detected on Myoporum sp. and Viburnum tinus [1]. Here, we report the high-quality genome sequence of an ST88 strain and the complete circular genome sequence of an ST89 strain by combining PacBio and Illumina sequencing data. In addition, we performed a phylogenomic analysis of the subspecies multiplex to investigate the phylogenetic position and potential origin of these new strains.

## 3. Data Description

Long- and short-reads were obtained via the PacBio HiFi and Illumina platforms, respectively. The final assemblies resulted in a single non-circularized contig for the ST88 strain LSV52.37 and a complete circular genome for the ST89 strain LSV52.52 (Table 1). No plasmids were detected in either genome. The genome of the ST88 strain was longer than the genome of the ST89 strain (2.69 Mbp and 2.52 Mbp, respectively) but both genomes are in the typical size range for X. fastidiosa genomes. The number of pseudogenes was very low (25 and 32, respectively) and CheckM confirmed a high genome completeness and absence of contamination (Table 1). The

<caption>**Table 1**</caption>

Genome assembly and annotation metrics of the two Xylella fastidiosa subsp. multiplex ST88 and ST89 strains.

<table><thead><tr><th>Metrics</th><th>LSV52.37 (ST88)</th><th>LSV52.52 (ST89)</th></tr></thead><tbody><tr><td>Nb of reads (PacBio/Illumina)</td><td>56,996 / 3,967,328</td><td>69,832 / 3,895,010</td></tr><tr><td>Genome size (bp)</td><td>2,698,430</td><td>2,524,893</td></tr><tr><td>Nb of contigs</td><td>1</td><td>1</td></tr><tr><td>GC (%)</td><td>51.77</td><td>51.81</td></tr><tr><td>Coverage (long reads)</td><td>171</td><td>243</td></tr><tr><td>Coverage (short reads)</td><td>282</td><td>256</td></tr><tr><td>CDS</td><td>2679</td><td>2409</td></tr><tr><td>Pseudogenes</td><td>25</td><td>32</td></tr><tr><td>rRNA</td><td>6</td><td>6</td></tr><tr><td>tRNA</td><td>55</td><td>54</td></tr><tr><td>tmRNA</td><td>1</td><td>1</td></tr><tr><td>ncRNA</td><td>9</td><td>6</td></tr><tr><td>Regulatory ncRNA</td><td>2</td><td>2</td></tr><tr><td>CheckM Completeness (%)</td><td>99.28</td><td>99.64</td></tr><tr><td>CheckM Contamination (%)</td><td>0.00</td><td>0.00</td></tr><tr><td>BioProject</td><td>PRJNA1234384</td><td>PRJNA1234386</td></tr></tbody></table>
<caption>**Table 2**</caption>

Genome sequences of *X. fastidiosa* subsp. *multiplex* strains available in GenBank used for the phylogenomic analysis.

<table><thead><tr><th>Strain name</th><th>ST</th><th>Host plant</th><th>Location</th><th>Accession</th></tr></thead><tbody><tr><td>CFBP8418</td><td>6</td><td>Spartium junceum</td><td>France: Corsica</td><td>GCF_042244175.1</td></tr><tr><td>CFBP8417</td><td>6</td><td>Spartium junceum</td><td>France: Corsica</td><td>GCF_042244685.1</td></tr><tr><td>Dixon</td><td>6</td><td>Prunus dulcis</td><td>USA: California</td><td>GCF_029626005.1</td></tr><tr><td>ESVL</td><td>6</td><td>Prunus dulcis</td><td>Spain: Alicante</td><td>GCF_004023385.1</td></tr><tr><td>IVIA5901</td><td>6</td><td>Prunus dulcis</td><td>Spain: Alicante</td><td>GCF_004023395.2</td></tr><tr><td>IVIA6586-2</td><td>6</td><td>Helichrysum italicum</td><td>Spain: Alicante</td><td>GCF_009669335.1</td></tr><tr><td>IVIA6731</td><td>6</td><td>Helichrysum italicum</td><td>Spain: Alicante</td><td>GCF_009669375.1</td></tr><tr><td>NZ4_CA</td><td>6</td><td>Brachyglottis compacta</td><td>USA: California</td><td>GCF_043355825.1</td></tr><tr><td>CFBP8416</td><td>7</td><td>Polygala myrtifolia</td><td>France: Corsica</td><td>GCF_001971475.1</td></tr><tr><td>CFBP8433</td><td>7</td><td>Cistus monspeliensis</td><td>France: Corsica</td><td>GCF_028752655.1</td></tr><tr><td>Griffin-1</td><td>7</td><td>Quercus rubra</td><td>USA: Georgia</td><td>GCA_000466025.1</td></tr><tr><td>LM10</td><td>7</td><td>Olea europaea</td><td>USA: California</td><td>GCF_012974145.1</td></tr><tr><td>M12</td><td>7</td><td>Prunus dulcis</td><td>USA: California</td><td>GCF_000019325.1</td></tr><tr><td>RAAR6 Butte</td><td>7</td><td>Prunus dulcis</td><td>USA: California</td><td>GCF_009695485.1</td></tr><tr><td>Red Oak 2</td><td>7</td><td>Quercus rubra</td><td>USA: Georgia</td><td>GCF_015475935.1</td></tr><tr><td>Red Oak 8</td><td>7</td><td>Quercus rubra</td><td>USA: Georgia</td><td>GCF_021459885.1</td></tr><tr><td>RH1</td><td>7</td><td>Olea europaea</td><td>USA: California</td><td>GCF_012974125.1</td></tr><tr><td>sycamore Sy-VA</td><td>8</td><td>Platanus occidentalis</td><td>USA: Virginia</td><td>GCF_000732705.1</td></tr><tr><td>GaTree2</td><td>8</td><td>Carya illinoinensis</td><td>USA: Georgia</td><td>GCA_042862445.1</td></tr><tr><td>Oak 35874</td><td>9</td><td>Quercus sp.</td><td>USA: Washington</td><td>GCF_021459905.1</td></tr><tr><td>CFBP8070</td><td>10</td><td>Prunus sp.</td><td>USA: Georgia</td><td>GCF_042243345.1</td></tr><tr><td>P5A2</td><td>10</td><td>Prunus persica</td><td>USA: Alabama</td><td>GCA_022548865.1</td></tr><tr><td>RAAR14 plum327</td><td>26</td><td>Prunus domestica</td><td>Brazil: Rio Grande do Sul</td><td>GCF_009695495.1</td></tr><tr><td>CFBP8075</td><td>27</td><td>Prunus sp.</td><td>USA: California</td><td>GCF_042242545.1</td></tr><tr><td>Riv5</td><td>34</td><td>Prunus cerasifera</td><td>USA: California</td><td>GCF_015475955.1</td></tr><tr><td>CFBP8173 (ATCC 35871)</td><td>41</td><td>Prunus salicina</td><td>USA: Georgia</td><td>GCF_042241145.1</td></tr><tr><td>ICMP8740</td><td>41</td><td>Platanus occidentalis</td><td>USA: Washington</td><td>GCF_028735895.1</td></tr><tr><td>CFBP8068 (ATCC 35873)</td><td>41</td><td>Ulmus sp.</td><td>USA: Washington</td><td>GCF_042241895.1</td></tr><tr><td>AlmaEm3</td><td>42</td><td>Vaccinium sp.</td><td>USA: Georgia</td><td>GCF_018069645.1</td></tr><tr><td>BB01</td><td>42</td><td>Vaccinium corymbosum</td><td>USA: Georgia</td><td>GCF_001886315.1</td></tr><tr><td>LA-Y3C</td><td>42</td><td>Vaccinium virgatum</td><td>USA: Louisiana</td><td>GCF_021459845.1</td></tr><tr><td>BBI64</td><td>42</td><td>Vaccinium sp.</td><td>USA: Georgia</td><td>GCA_006369955.1</td></tr><tr><td>BB08-1</td><td>43</td><td>Vaccinium "Windsor"</td><td>USA: Florida</td><td>GCF_018069665.1</td></tr><tr><td>CFBP8078</td><td>51</td><td>Vinca sp.</td><td>USA: Florida</td><td>GCF_004016365.1</td></tr><tr><td>Fillmore</td><td>81</td><td>Olea europaea</td><td>USA: California</td><td>GCF_012974105.1</td></tr><tr><td>XF3348</td><td>81</td><td>Prunus dulcis</td><td>Spain: Majorca</td><td>GCF_042239545.1</td></tr><tr><td>XYL1966/18</td><td>81</td><td>Olea europaea</td><td>Spain: Minorca</td><td>GCF_042238405.1</td></tr><tr><td>XYL1981</td><td>81</td><td>Ficus carica</td><td>Spain: Majorca</td><td>GCF_009669455.1</td></tr><tr><td>Santa29b</td><td>81</td><td>Santolina chamaecyparissus</td><td>Spain: Minorca</td><td>GCF_042240315.1</td></tr><tr><td>Ma1</td><td>87</td><td>Rhamnus alaternus</td><td>Italy: Tuscany</td><td>GCF_018449155.1</td></tr><tr><td>Ma26</td><td>87</td><td>Spartium junceum</td><td>Italy: Tuscany</td><td>GCF_018449175.1</td></tr><tr><td>Ma29</td><td>87</td><td>Prunus dulcis</td><td>Italy: Tuscany</td><td>GCF_018449135.1</td></tr><tr><td>Ma185</td><td>87</td><td>Polygala myrtifolia</td><td>Italy: Tuscany</td><td>GCF_018449105.1</td></tr><tr><td>NZ13_CA</td><td>88</td><td>Pomaderris prunifolia</td><td>USA: California</td><td>GCF_043195255.1</td></tr></tbody></table>

genome assemblies and the raw sequencing data were deposited in the NCBI databases under BioProject numbers PRJNA1234384 for *X. fastidiosa* subsp. *multiplex* ST88 (strain LSV52.37) and PRJNA1234386 for *X. fastidiosa* subsp. *multiplex* ST89 (strain LSV 52.52). A phylogenomic analysis based on SNPs was performed using the two genomes obtained in this study and 44 genome sequences representing the genetic diversity of the subspecies *multiplex* available in GenBank as of 12/12/2024 (Table 2, Fig. 1).

This analysis revealed that the ST88 strain (LSV52.37) isolated from *Polygala myrtifolia* in France clustered with another ST88 strain (NZ13_CA) recently isolated from *Pomaderris prunifolia* in California (USA) [7]. The two ST88 strains formed a highly-supported clade most closely related to ST7 strains from Red Oak and almond isolated in the USA. In contrast, the ST89 strain (LSV52.52) was closely-related to American ST27 infecting almond and plum.
<figure><img src="image_3.png" /><figcaption>**Fig. 1.** Phylogenomic tree showing the relationships of *X. fastidiosa* subsp. *multiplex* strains using maximum likelihood analysis. The tree was visualized using FigTree. Strains sequenced in this study are in bold. Bootstraps > 80% are represented by grey stars.</figcaption></figure>

# 4. Experimental Design, Materials and Methods

## 4.1. Bacterial Culture

*Xylella fastidiosa* subsp. *multiplex* strain LSV52.37 (ST88) was isolated in 2020 from *Polygala myrtifolia* in Saint-Raphaël (PACA region) and LSV52.52 (ST89) was isolated in 2021 from *Myoporum* sp. in Villeneuve-Loubet (PACA region) on modified PWG (Periwinkle Wilt-Gelrite) medium [2]. They are stored at -80°C in the laboratory collection of the ANSES Plant Health Laboratory.

## 4.2. DNA Extraction and Library Preparation

For PacBio long-read sequencing, bacteria were grown on solid PWG medium at 28°C for seven days. The cultures were replated twice to obtain sufficient bacterial cells. Bacterial cells from these plate cultures were suspended in 10 mL of sterile water with DO₆₀₀ 0.3-0.6. Genomic DNA was extracted from these bacterial suspensions using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA), following the protocol for Gram-positive bacteria with some modifications to improve cell lysis and DNA purity: the initial bacterial cell pellet was washed once in 2 mL of sterile water before being resuspended in 480 µL EDTA (50 mM, pH=8). Lysozyme (120 µL, 10 mg/mL) was then added, followed by incubation at 37°C for 60 min. 35 µL of Pronase (5 mg/mL) was added and the samples incubated overnight at 37°C. Next, 150 µL of 10% SDS (w/v) was added and the samples were incubated at 37°C for 45 min. Nuclei Lysis Solution (800 µL) was then added and the samples were incubated at 80°C for 5 min. Following RNase A treatment at 37°C for 60 min, 270 µL of Protein Lysis Solution was added and incubated on ice for 20 min. After centrifugation at 16,000 g for 6 min, DNA was precipitated in 1 volume of isopropanol, the DNA pellet was washed once with 70% ethanol (v/v) and resuspended in DNA Rehydration Solution. DNA quality was verified using a Nanodrop One (Thermo Fisher Scientific, Waltham,
USA) and DNA concentration was quantified using the Qubit dsDNA Broad Range assay kit (Invitrogen, Waltham, USA). Library preparation and sequencing on the PacBio HiFi platform were performed by the Gentyane sequencing facility at Clermont-Ferrand, France. For Illumina sequencing, bacteria were grown on solid modified PWG medium at 28°C for seven days. The cultures were replated twice to obtain sufficient bacterial cells. Bacterial cells from these plate cultures were suspended in 1 mL of sterile water at a concentration of 10⁹ CFU/mL. Genomic DNA was extracted from these bacterial suspensions using the QuickPick™ SML Plant DNA kit (Bio-Nobile, Pargas, Finland). Illumina sequencing libraries were generated as previously described [8].

## 4.3. Sequencing Analysis

Long-read assemblies were performed using both Canu v2.1.1 [9] and Flye v2.8.1 [10]. For the strain LSV52.37 (ST88), the most contiguous assembly was obtained using Canu with the parameters `genomeSize=2.7m`, `minReadLength=2000`, `minOverlapLength=1000`, producing two contigs. Using the Illumina reads, these two contigs were scaffolded into a single contig with Redundans v0.14 [11] with the parameters `-noreduction -limit 1`. Circularization was attempted using Circlator v1.5.6 [12] but was not successful. The genome of the strain LSV52.52 (ST89) was directly assembled into a single circular contig using Flye with the parameters `-pacbio-hifi`, `-g 2.7m` and `-min-overlap 1000`. The genome was rotated to start with the gene `dnaA` using Circlator's `fixstart` function. Both assemblies were polished with the Illumina reads using Polca from the MaSuRCa toolkit v4.0.9 [13], but no errors were found, confirming the high quality of the PacBio HiFi assemblies. Genome completeness and contamination was verified using CheckM v1.1.6 [14] and both genomes were annotated using Bakta v1.5.1 [15] (Table 1). Coverage was estimated using Mosdepth [16] as implemented on Galaxy (usegalaxy.org). Default parameters were used for all bioinformatics tools unless stated otherwise.

## 4.4. Phylogenomic Analysis

Multiple genome alignment of all assemblies (Table 2) was performed using Parsnp v1.5.6 [17]. An in-house python script (supplementary data) was used to concatenate blocks in the `xmfa` file to obtain a `fasta` file. Recombination tracts were removed from the alignment using `ClonalFrameML` v1.12 [18]. The maximum likelihood phylogenetic tree was obtained using IQ-TREE v2.0.3 [19]. The best substitution model was inferred directly by JModelTest [20] implemented in IQ-TREE, and the values of branch support were obtained by bootstrap method using 1000 replicates. The final phylogenetic tree was visualized using FigTree v1.4.4 (https://github.com/rambaut/figtree).

## Limitations

None.

## Ethics Statement

The authors have read and follow the ethical requirements for publication in Data in Brief. The current work does not involve human subjects, animal experiments, or any data collected from social media platforms
## Data Availability

Xylella fastidiosa ST89 genome sequencing and assembly (NCBI) (Original data).

Xylella fastidiosa ST88 genome sequencing and assembly (NCBI) (Original data).

## CRediT Author Statement

**Amandine Cunty:** Conceptualization, Methodology, Writing – original draft; **Jessica Dittmer:** Methodology, Writing – original draft; **Déborah Merda:** Formal analysis, Writing – review & editing; **Bruno Legendre:** Writing – review & editing; **Benoît Remenant:** Writing – review & editing; **Yannick Blanchard:** Writing – review & editing; **Sophie Cesbron:** Methodology, Writing – review & editing; **Marie-Agnès Jacques:** Funding acquisition, Writing – review & editing; **Pascal Gentit:** Funding acquisition, Writing – review & editing; **Anne-Laure Boutigny:** Conceptualization, Methodology, Writing – review & editing.

## Acknowledgements

We would like to thank the SPAAD (shared service and support for data analysis) for making their calculation server available and storing the data. We are grateful to the computing clusters of the IRHS providing computing resources. The authors would like to thank Jas Hennessy & Cie for financial support of part of this research.

## Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

## Supplementary Materials

Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.dib.2025.111816.

## References

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[2] EPPO, PM 7/24 (5) *Xylella fastidiosa*, EPPO Bull. 53 (2023) 205–276, doi:10.1111/epp.12923.

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