Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain

Giampetruzzi, Annalisa; Chiumenti, Michela; Saponari, María; Donvito, Giacinto; Italiano, Alessandro; Loconsole, Giuliana; Boscia, D.; Cariddi, C.; Martelli, G. P.; Saldarelli, P.

doi:10.1128/genomea.01538-14

Cited by 58 publications

(68 citation statements)

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“…pauca in Central America (Nunney et al 2014b). Likewise, the recent emergence of X. fastidiosa in Europe (Giampetruzzi et al 2015a;Saponari et al 2013) illustrates the potential for long-distance dispersal of this bacterium and the vulnerability of the Mediterranean landscape and agriculture to invasion by new organisms.…”

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Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

et al. 2017

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Xylella fastidiosa is a plant-pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles that are monophyletic with those of subsp. pauca in South America. To more robustly determine the phylogenetic placement of ST53 within X. fastidiosa, we performed a comparative analysis based on single nucleotide polymorphisms (SNPs) and the study of the pan-genome of the 27 currently public available whole genome sequences of X. fastidiosa. The resulting maximum-parsimony and maximum likelihood trees constructed using the SNPs and the pan-genome analysis are consistent with previously described X. fastidiosa taxonomy, distinguishing the subsp. fastidiosa, multiplex, pauca, sandyi, and morus. Within the subsp. pauca, the Italian and three Costa Rican isolates, all belonging to ST53, formed a compact phylotype in a clade divergent from the South American pauca isolates, also distinct from the recently described coffee isolate CFBP8072 imported into Europe from Ecuador. These findings were also supported by the gene characterization of a conjugative plasmid shared by all the four ST53 isolates. Furthermore, isolates of the ST53 clade possess an exclusive locus encoding a putative ATP-binding protein belonging to the family of histidine kinase-like ATPase gene, which is not present in isolates from the subspecies multiplex, sandyi, and pauca, but was detected in ST21 isolates of the subspecies fastidiosa from Costa Rica. The clustering and distinctiveness of the ST53 isolates supports the hypothesis of their common origin, and the limited genetic diversity among these isolates suggests this is an emerging clade within subsp. pauca.

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Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

et al. 2017

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“…Only recently two olive cultivars, Leccino and Favolosa FS-17 were selected, that appear to have some degree of tolerance to the disease (Giampetruzzi et al, 2016). The introduction in Puglia of X. fastidiosa could be due to infected plant material imported from Central America (Giampetruzzi et al, 2015a; Marcelletti and Scortichini, 2016b). Other recent reports describe the presence of X. fastidiosa in olive trees showing leaf scorch symptoms in Argentina (Haelterman et al, 2015) and Brazil (Della Coletta et al, 2016).…”

Section: Hosts and Diseasesmentioning

confidence: 99%

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques

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2017

Front. Plant Sci.

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In the never ending struggle against plant pathogenic bacteria, a major goal is the early identification and classification of infecting microorganisms. Xylella fastidiosa, a Gram-negative bacterium belonging to the family Xanthmonadaceae, is no exception as this pathogen showed a broad range of vectors and host plants, many of which may carry the pathogen for a long time without showing any symptom. Till the last years, most of the diseases caused by X. fastidiosa have been reported from North and South America, but recently a widespread infection of olive quick decline syndrome caused by this fastidious pathogen appeared in Apulia (south-eastern Italy), and several cases of X. fastidiosa infection have been reported in other European Countries. At least five different subspecies of X. fastidiosa have been reported and classified: fastidiosa, multiplex, pauca, sandyi, and tashke. A sixth subspecies (morus) has been recently proposed. Therefore, it is vital to develop fast and reliable methods that allow the pathogen detection during the very early stages of infection, in order to prevent further spreading of this dangerous bacterium. To this purpose, the classical immunological methods such as ELISA and immunofluorescence are not always sensitive enough. However, PCR-based methods exploiting specific primers for the amplification of target regions of genomic DNA have been developed and are becoming a powerful tool for the detection and identification of many species of bacteria. The aim of this review is to illustrate the application of the most commonly used PCR approaches to X. fastidiosa study, ranging from classical PCR, to several PCR-based detection methods: random amplified polymorphic DNA (RAPD), quantitative real-time PCR (qRT-PCR), nested-PCR (N-PCR), immunocapture PCR (IC-PCR), short sequence repeats (SSRs, also called VNTR), single nucleotide polymorphisms (SNPs) and multilocus sequence typing (MLST). Amplification and sequence analysis of specific targets is also mentioned. The fast progresses achieved during the last years in the DNA-based classification of this pathogen are described and discussed and specific primers designed for the different methods are listed, in order to provide a concise and useful tool to all the researchers working in the field.

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“…Symptoms of OQDS include yellow and brown lesions on leaf tips and margins, extensive branch and twig dieback, and subsequent tree mortality (1). Genome data and multilocus sequence typing (MLST) analyses (2, 3) showed that olive-infecting isolates of X. fastidiosa were genetically related to subspecies pauca and all harbored the sequence type 53 (ST53). In this report, we describe the complete and finished genome sequence of X. fastidiosa subsp.…”

Section: Genome Announcementmentioning

confidence: 99%

Complete Genome Sequence of the Olive-Infecting Strain Xylella fastidiosa subsp. pauca De Donno

et al. 2017

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Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain

Abstract: We determined the draft genome sequence of the Xylella fastidiosa CoDiRO strain, which has been isolated from olive plants in southern Italy (Apulia). It is associated with olive quick decline syndrome (OQDS) and characterized by extensive scorching and desiccation of leaves and twigs.

Cited by 58 publications

References 11 publications

Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques

Complete Genome Sequence of the Olive-Infecting Strain Xylella fastidiosa subsp. pauca De Donno

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