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

HomePhytopathology®Vol. 113, No. 1Draft Genome Sequence Resource of Xylella fastidiosa Strain Alm_Lz_1 Associated with a New Outbreak in Lazio, Italy Previous Resource Announcement OPENOpen Access licenseDraft Genome Sequence Resource of Xylella fastidiosa Strain Alm_Lz_1 Associated with a New Outbreak in Lazio, ItalyAnnalisa Giampetruzzi, Giuliana Loconsole, Stefania Zicca, Donato Boscia, Giorgio Mariano Balestra, and Maria SaponariAnnalisa GiampetruzziIstituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, ItalySearch for more papers by this author, Giuliana LoconsoleIstituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, ItalySearch for more papers by this author, Stefania ZiccaIstituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, ItalySearch for more papers by this author, Donato BosciaIstituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, ItalySearch for more papers by this author, Giorgio Mariano BalestraDipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, 01100, Viterbo, ItalySearch for more papers by this author, and Maria Saponari†Corresponding author: M. Saponari; E-mail Address: [email protected]https://orcid.org/0000-0002-4563-8089Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, ItalySearch for more papers by this authorAffiliationsAuthors and Affiliations Annalisa Giampetruzzi1 Giuliana Loconsole1 Stefania Zicca1 Donato Boscia1 Giorgio Mariano Balestra2 Maria Saponari1 † 1Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy 2Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, 01100, Viterbo, Italy Published Online:14 Dec 2022https://doi.org/10.1094/PHYTO-05-22-0185-AAboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Genome AnnouncementIn 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 850×.Whole genome comparison by Roary tool (v3.11.2) (Page et al. 2015) was used to generate alignments of accessory and core genes between subsp. multiplex strains (Table 1) and the newly sequenced Alm_Lz_1 strains (1,378 core genes, 3,385 accessory genes) re-annotated by Prokka tool (Seemann 2014).Table 1. Xylella fastidiosa subsp. multiplex strains used for genomic comparisonaStrainSTHostLocationAssembly accessionAssembly lengthAssembly levelSubmission dateOrthoANIu value (%)Average aligned length (bp)CFBP84176Spartium junceumFrance: CorsicaGCF_001971505.12,504,981Contig25/01/2017……CFBP84186Spartium junceumFrance: CorsicaGCF_001971465.12,513,969Contig25/01/2017……Dixon6Prunus dulcisUSA: CaliforniaGCF_000166835.12,622,328Scaffold26/07/2005……ESVL6Prunus dulcisSpain: AlicanteGCF_004023385.12,554,495Contig16/01/2019……IAS_AXF_212H76Prunus dulcisSpain: AlicanteGCF_009669445.12,522,542Contig18/11/2019……IAS_AXF_235T106Prunus dulcisSpain: AlicanteGCF_009669465.12,550,209Contig18/11/2019……IVIA59016Prunus dulcisSpain: AlicanteGCF_004023395.22,559,157Complete genome27/08/2020……IVIA6586_26Helicrysum italicumSpain: Alicante GCF_009669335.12,578,155Contig18/11/2019……IVIA66296Rhamnus alaternusSpain: Alicante GCF_009669365.12,731,703Contig18/11/2019……IVIA67316Helichrysum italicumSpain: Alicante GCF_009669375.12,598,893Contig18/11/2019……IVIA69026Prunus dulcisSpain: Alicante GCF_009669405.12,870,108Contig18/11/2019……IVIA69036Prunus dulcisSpain: Alicante GCF_009669425.12,602,829Contig18/11/2019……Griffin_17Quercus rubraUSAGCA_000466025.12,387,314Contig09/12/2013……LM107Olea europaea ornamentalUSA: CaliforniaGCF_012974145.12,669,650Complete genome05/05/2020……M127Prunus dulcisUSA: CaliforniaGCF_000019325.12,475,130Complete genome19/02/2008……RAAR6_Butte7Prunus dulcisUSA: CaliforniaGCF_009695485.12,466,226Contig22/11/2019……Red_Oak_27Quercus rubraUSA: GeorgiaGCF_015475935.12,476,446Complete genome15/11/2020……Red_Oak_87Quercus rubraUSA: GeorgiaGCF_021459885.12,476,438Complete genome13/01/2022……RH17Olea europaea ornamentalUSA: CaliforniaGCF_012974125.12,678,425Complete genome05/05/2020……Sycamore_Sy_VA8Platanus occidentalisUSA: VirginiaGCF_000732705.12,475,880Contig22/07/2014……Oak_358749QuercusUSA: Washington DCGCF_021459905.12,648,027Complete genome13/01/2022……Riv534Ornamental plumUSA: CaliforniaGCF_015475955.12,538,293Complete genome15/11/2020……ATCC 3587141Prunus salicinaUSA: CaliforniaGCF_000428665.12,416,255Scaffold15/07/2013……AlmaEM342VacciniumUSA: GeorgiaGCF_018069645.12,487,451Complete genome18/04/2021……BB0142Vaccinium corymbosumUSA: CaliforniaGCF_001886315.12,511,521Scaffold25/11/2016……LA_Y3C42Vaccinium virgatumUSA: LouisianaGCF_021459845.12,526,390Complete genome13/01/2022……BB08_143Vaccinium ‘Windsor’USA: FloridaGCF_018069665.12,553,631Complete genome18/04/2021……Fillmore81Olea europaeaUSA: CaliforniaGCF_012974105.12,526,544Complete genome05/05/2020……XF_3960_1881Prunus dulcisSpain: MallorcaGCF_014856905.12,518,024Scaffold06/10/2020……XF334881Prunus dulcisSpain: MallorcaGCF_009669515.12,573,395Contig18/11/2019……XYL175281Prunus dulcisSpain: MenorcaGCF_009669505.12,579,375Contig18/11/2019……XYL1966_1881Olea europaea var. europaeaSpain: MenorcaGCF_014856865.12,514,978Scaffold06/10/2020……XYL1968_1881Olea europaea var. europaeaSpain: MenorcaGCF_014856935.12,518,610Contig06/10/2020……XYL198181Ficus caricaSpain: MallorcaGCF_009669455.12,554,510Contig18/11/2019……XYL1981_1881Prunus dulcisSpain: MallorcaGCF_014856675.12,509,949Scaffold06/10/2020……RAAR14_plum32726Prunus domesticaBrazilGCF_009695495.12,543,559Contig22/11/201999.501,863,808CFBP807851Vinca sp.USA: FloridaGCF_004016365.12,596,546Contig14/01/201999.461,728,174Ma187Rhamnus alaternusItaly: Monte ArgentarioGCF_018449155.12,414,358Contig23/05/202199.951,813,277Ma1087Rhamnus alaternusItaly: Monte ArgentarioGCF_018449235.12,415,263Contig23/05/202199.921,846,455Ma15187Rhamnus alaternusItaly: Monte ArgentarioGCF_018449095.12,416,213Contig23/05/202199.951,754,534Ma18587Polygala myrtifoliaItaly: Monte ArgentarioGCF_018449105.12,412,610Contig23/05/202199.941,887,469Ma2687Spartium junceumItaly: Monte ArgentarioGCF_018449175.12,412,928Contig23/05/202199.941,840,637Ma2987Prunus dulcisItaly: Monte ArgentarioGCF_018449135.12,426,899Contig23/05/202199.971,840,787TOS1487Spartium junceum L.Italy: TuscanyGCF_007713995.12,445,518Contig30/07/201999.971,997,217TOS487Prunus dulcisItaly: TuscanyGCF_007713905.12,445,114Contig30/07/201999.971,939,344TOS587Polygala myrtifoliaItaly: TuscanyGCF_007713945.12,443,867Contig30/07/201999.982,002,073Alm_Lz_187Prunus dulcisItaly: LazioThis study2,458,683ContigThis study aST, sequence type. OrthoANIu value (%) and average aligned length values were calculated only for the 11 closest strains to Alm_Lz_1.Table 1. Xylella fastidiosa subsp. multiplex strains used for genomic comparisonaView as image HTML All ST87 genomes were grouped in a monophyletic cluster considering the tree on core genes alignment by RAxML (Stamatakis 2014) (Fig. 1A). Moreover, considering the phylogenomic tree on accessory genes, within the group of ST87 strains previously described in Tuscany from different hosts, Alm_Lz_1 clustered with the strain TOS4 (Fig. 1B), a strain originally isolated from P. dulcis (Saponari et al. 2019) (Table 1).Fig. 1. Phylogenomic trees. A, RAxML final bootstrap tree (midpoint rooted) calculated from the Roary core-genome alignment of all Xylella fastidiosa subsp. multiplex genomes. Sequence type (ST)87 clade is highlighted in gray by FigTree v1.4.4 tool (http://tree.bio.ed.ac.uk/software/figtree/). B, Tree based on the binary presence/absence matrix of accessory genes built by Roary and proportionally transformed with Figtree (http://tree.bio.ed.ac.uk/software/figtree/). Scale is number of substitutions per site.Download as PowerPointFunctional annotation by submission to the NCBI Prokaryotic Genome Automatic Annotation Pipeline resulted in the identification of six rRNA genes (two operons), 49 tRNA loci, 2,256 genes, 2,196 protein-encoding genes, and three noncoding RNAs in the draft genome of the strain Alm_Lz_1. No circular contigs were detected by in silico analysis.The genome sequences produced for strain Alm_Lz_1, isolated in Lazio, Italy, further contribute to extend and to implement the genomic data available for isolates harboring ST87 profile among the European strains of X. fastidiosa subsp. multiplex (Román-Reyna et al. 2021). These data, coupled with different sources of information, such as the monitoring data, can help to gather more insights into the dynamics of Xylella species, by elucidating putative pathway(s) and event(s) of introduction in Europe and by understanding the main drivers of the infections.Data AvailabilityThe genome sequences of X. fastidiosa strain Alm_Lz_1 have been deposited as GenBank accession number JALHBT000000000 in BioProject PRJNA820720.AcknowledgmentsWe thank the Servizio Fitosanitario Regionale, Direzione Regionale Agricoltura, Promozione della Filiera e della Cultura del Cibo, Caccia e Pesca, Foreste, Regione Lazio for the fruitful collaboration. This work was conducted using bioinformatic analysis equipment from the datacenter ReCaS of the University of Bari Aldo Moro.The author(s) declare no conflict of interest.Literature CitedAntipov, D., Raiko, M., Lapidus, A., and Pevzner, P. A. 2019. Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res. 29:961-968. https://doi.org/10.1101/gr.241299.118 Crossref, Medline, ISI, Google ScholarBankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin,V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V.,Vyahhi, N., Tesler, G., Alekseyev, M. A., and Pevzner, P. A. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455-477. https://doi.org/10.1089/cmb.2012.0021 Crossref, Medline, ISI, Google ScholarGiampetruzzi, A., D'Attoma, G., Zicca, S., Kubaa, R. A., Rizzo, D., Boscia, D., Saldarelli, P., and Saponari, M. 2019. Draft genome sequence resources of three strains (TOS4, TOS5, and TOS14) of Xylella fastidiosa infecting different host plants in the newly discovered outbreak in Tuscany, Italy. Phytopathology 109:1516-1518. https://doi.org/10.1094/PHYTO-04-19-0108-A Link, ISI, Google ScholarMarchi, G., Rizzo, D., Ranaldi, F., Ghelardini, L., Ricciolini, M., Scarpelli, I., Drosera, L., Goti, E., Capretti, P., and Surico, G. 2018. First detection of Xylella fastidiosa subsp. multiplex DNA in Tuscany (Italy). Phytopathol. Mediterr. 57:363-364. ISI, Google ScholarPage, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T. G., Fookes, M., Falush, D., Keane, J. A., and Parkhill, J. 2015. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691-3693. https://doi.org/10.1093/bioinformatics/btv421 Crossref, Medline, ISI, Google ScholarRomán-Reyna, V., Dupas, E., Cesbron, S., Marchi, G., Campigli, S., Hansen, M. A., Bush, E., Prarat, M., Shiplett, K., Ivey, M. L. L., Pierzynski, J., Miller, S. A., Peduto Hand, F., Jacques, M. A., and Jacobs, J. M. 2021. Metagenomic sequencing for identification of Xylella fastidiosa from leaf samples. mSystems 6:e0059121. https://doi.org/10.1128/mSystems.00591-21 Crossref, Medline, ISI, Google ScholarSaponari, M., D'Attoma, G., Abou Kubaa, R., Loconsole, G., Altamura, G., Zicca, S., Rizzo, D., and Boscia, D. 2019. A new variant of Xylella fastidiosa subspecies multiplex detected in different host plants in the recently emerged outbreak in the region of Tuscany, Italy. Eur. J. Plant Pathol. 154:1195-1200. https://doi.org/10.1007/s10658-019-01736-9 ISI, Google ScholarSeemann, T. 2014. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069. https://doi.org/10.1093/bioinformatics/btu153 Crossref, Medline, ISI, Google ScholarStamatakis, A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313. https://doi.org/10.1093/bioinformatics/btu033 Crossref, Medline, ISI, Google ScholarWells, J. M., Raju, B. C., Nyland, G., and Lowe, S. K. 1981. Medium for isolation and growth of bacteria associated with plum leaf scald and phony peach diseases. Appl. Environ. Microbiol. 42:357-363. https://doi.org/10.1128/aem.42.2.357-363.1981 Crossref, Medline, ISI, Google ScholarThe author(s) declare no conflict of interest.DetailsFiguresLiterature CitedRelated Vol. 113, No. 1 January 2023SubscribeISSN:0031-949Xe-ISSN:1943-7684 DownloadCaptionLeaf deformation, tip necrosis and twisting, and overall stunting 28 days after agroinfiltration of tobacco, Nicotiana occidentalis, with blueberry virus S (Villamor et al.). Photo credit: Dan Villamor Metrics Article History Issue Date: 25 Jan 2023Published: 14 Dec 2022Accepted: 18 Aug 2022 Pages: 108-111 Information© 2022 The American Phytopathological SocietyKeywordsbacterial pathogensmicrobe-genome sequencingmultiplexST87Xylella fastidiosaThe author(s) declare no conflict of interest.PDF download