Xylella fastidiosa (Xf) is a xylem-limited quarantine phytobacterium representing a serious threat to European and Mediterranean agriculture and landscape, where outbreaks caused by strains belonging to three subspecies have been reported in Italy, France, Spain, Portugal, Israel, Iran and Lebanon (PM 7/24 (5) Xylella fastidiosa, 2023).
In Italy, isolates harbouring the sequence type (ST) 53, were first detected in 2013 in the Apulia region, infecting mainly olives but also numerous species of the Mediterranean flora (Loconsole et al. 2016; Saponari et al. 2019), then rapidly spreading and causing the severe epidemic of olive quick decline syndrome. In the framework of the intensive surveillance program ongoing in this region, targeting mainly the buffer zone and pest-free area, an outbreak of Xylella fastidiosa subsp. fastidiosa (Xff) was intercepted in early 2024 in the pest free area (Cornara et al. 2024). Grapes and almond turned to be the most frequent infected host species.
Two strains were cultured from dormant canes of Vitis vinifera (BA_GR31, Lat. 41.07476179; Lon. 16.94624537), and hardwood shoots of Prunus dulcis (BA_AL21, Lat. 41.06968633; Lon 16.94135367) collected in early spring 2024. Multilocus sequence typing analyses (Yuan et al. 2010) performed on total plant DNA indicated that the infection was associated with an isolate genetically related to subsp. fastidiosa and harboring the genotype ST1, the most frequent genotype associated with the isolates causing the Pierce’s disease in North America (Van Sluys et al. 2003).
For genomic purposes, bacterial DNA from the two different strains was extracted from pure cultures grown on buffered charcoal-yeast extract (BCYE) agar medium (Wells et al. 1981) at 28 °C for 10 days and purified from the pelleted bacterial cells using a Qiagen DNeasy Plant Mini Kit according to the manufacturer’s instructions. The whole genome sequencing libraries were sequenced with a NovaSeq 6000 Illumina platform (150 bp paired-end) and with PacBio Sequel IIe system (Table 1). The quality of raw FASTQ paired reads (Illumina) and HiFi reads (PacBio) was evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). The two high-throughput datasets were combined for each strain using two different de novo assembly pipelines. The open-source assemblers Unicycler version 0.4.7 (Wick et al. 2017) and CANU v2.2 (Koren et al. 2017) were then run with the default options or following the default steps.