Draft Genome Sequence Resource of Xylella fastidiosa Strain Alm_Lz_1 Associated with a New Outbreak in Lazio, Italy

In November 2021, in the framework of the annual surveillance program implemented in all European Union countries, an outbreak of Xylella fastidiosa was intercepted in the Italian region of Lazio. The bacterium was detected in an almond tree (42°24 54.5 N, 11°38 49.4 E) showing typical bacterial leaf scorching. Subsequent in depth field surveys in the delimited area of the outbreak did not detect additional infected host plants. Multilocus sequence typing analyses performed on total DNA indicated that the infection was associated with an isolate genetically related to subsp. multiplex and harboring the sequence type (ST) ST87 (Marchi et al. 2018; Saponari et al. 2019). Isolates harboring the same ST were previously characterized in the outbreak discovered, in late 2018, in the neighbor region of Tuscany (approximately 30 to 50 km apart) (Saponari et al. 2019). So far, this genotype has been only reported from Italy and because of its recent discovery, only limited information is available regarding its biological features and no evidence is available regarding its place of origin (Giampetruzzi et al. 2019). A whole genome sequence resource will allow to exploit pangenome-oriented tools to get more insights into the biology of the strain (i.e., host plants under threat, pathogenicity) and to probe the pathway of introduction and its origin. In this report, we describe the draft genome sequences of X. fastidiosa strain Alm_Lz_1, obtained after its successful isolation in pure culture from a symptomatic tree of Prunus dulcis. Genomic DNA of strain Alm_Lz_1 was extracted from pure culture grown on buffered charcoal-yeast extract agar medium (Wells et al. 1981) using a commercial DNA purification kit. The whole genome sequencing library was paired-end sequenced with a NovaSeq 6000 Illumina platform. Illumina sequencing yielded a total of 14,027,398 high quality paired reads (2 × 150 bp) (Q30% of 92.23%). De novo genome assembly was done using SPAdes 3.13.0 (Bankevich et al. 2012) using multiple kmer (31,51,81,101,121) and trying to reduce the number of mismatches and short indels (careful option). The presence of contigs annotated as plasmid sequence was searched running plasmidSPAdes tool (Antipov et al. 2019). The final assemblies of the bacterial chromosomes resulted in 131 contigs, with an equal GC content of 51,73% (N50s was for 193,575). The average nucleotide coverage of the chromosomal genome was 850x.