Draft Genome Sequence of Xylella fastidiosa subsp.
            <i>fastidiosa</i>
            Strain IVIA5235, Isolated from Prunus avium in Mallorca Island, Spain

Landa, Blanca B.; Velasco-Amo, María Pilar; Marco‐Noales, Ester; Olmo, Diego; López, Marı́a M.; Navarro, Inmaculada; Monterde, Adela; Barbé, Silvia; Montes-Borrego, Miguel; Román-Écija, Miguel; Saponari, María; Giampetruzzi, Annalisa

doi:10.1128/mra.01222-18

Cited by 15 publications

(15 citation statements)

References 8 publications

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“…Additionally, the three isolates sequenced from cherry and grape from Mallorca, and all ST1 isolates from Mallorca tested so far, harbour the same plasmid as strain M23 of Xf subsp. fastidiosa ST1 isolated from almond in California (Landa et al , ; Gomila et al , ), providing additional support to the likely Californian origin of the ST1 introduction in Mallorca. There is evidence that almond–grapevine cross‐infections could be frequent, as in California (Almeida & Purcell, ), because PD isolates are capable of causing ALSD when mechanically inoculated (authors' unpublished observations).…”

Section: Discussionmentioning

confidence: 92%

“…As previously reported by Gomila et al (), a single circular plasmid sequence of 38 297 nucleotides was found in both strains XYL2055/17 and XYL1732/17, showing highest sequence similarities with the conjugative plasmids pXFAS01 (CP001012) and pXFAS_5235 (QWLC01), which were reported in Xf strain M23 (Chen et al , ) from almond and in Xf subsp. fastidiosa strain IVIA 5235 from cherry (Landa et al , ), respectively. Strain IVIA 5235 was isolated from Prunus avium in a garden centre in Mallorca that very likely became infected from neighbouring orchards affected by ALSD.…”

Section: Resultsmentioning

confidence: 99%

“…(QWLC01), which were reported in Xf strain M23 (Chen et al, 2010) from almond and in Xf subsp. fastidiosa strain IVIA 5235 from cherry (Landa et al, 2018), respectively. Strain IVIA 5235 was isolated from Prunus avium in a garden centre in Mallorca that very likely became infected from neighbouring orchards affected by ALSD.…”

Section: Transmission Experimentsmentioning

confidence: 99%

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Insights into the epidemiology of Pierce's disease in vineyards of Mallorca, Spain

Moralejo¹,

Borràs

Gomila

et al. 2019

Plant Pathology

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Xylella fastidiosa (Xf), the causal agent of Pierce's disease (PD), has long been considered a major threat to prosperous European viticulture. In May of 2017, PD was officially detected on a grapevine in Mallorca. To better understand the epidemiology of the first established outbreak of PD in Europe, the disease incidence and severity were assessed, vector transmission experiments were performed, and cultivar responses to Xf infections both in the field and in inoculation experiments were monitored. The genetic structure of Xf local populations was also investigated by multilocus sequence typing analysis, and their whole genome sequences and phylogenetic positions compared with respect to PD strains worldwide. Disease incidence was moderately low (0.07) and highly variable, ranging from 0.0 to 0.99. Its economic impact on wine production was considered low. Vineyards managed under conventional viticulture were significantly less infected than organic farming. Under greenhouse conditions, the insect Philaenus spumarius efficiently transmitted the pathogen from infected to healthy grapevines. In the inoculation experiments, Xf infected, to some degree, 29 of the 30 cultivar × rootstock combinations (n = 239). Cultivars Viura, Gorgollasa and Sauvignon Blanc were the most susceptible ones. All Xf isolates from grapevines belonged to sequence type ST1; they phylogenetically clustered within the Californian ST1 clade, with which they shared a 99.94% identity and the same plasmid. In addition, ST1 caused almond leaf scorch disease, where notably its incidence (0.78) and severity was much higher than PD. The likely reasons for these wide differences are discussed in the context of a 20‐year Xf introduction scenario.

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Section: Discussionmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

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Insights into the epidemiology of Pierce's disease in vineyards of Mallorca, Spain

Moralejo¹,

Borràs

Gomila

et al. 2019

Plant Pathology

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“…multiplex belonging to ST6 and ST7, which form a clonal complex integrated into a monophyletic clade 31,35 . The phylogeny and likely origin of these strains have been reviewed by Nunney et al 36,37 , and the complete genomes of several representative ALSD strains have been sequenced 29,38,39 . ST1 strains infect grapevines and can cross-infect almonds as well, whereas almond strains of ST6/7 do not cause disease on grapevines 30 .…”

mentioning

confidence: 99%

Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe

Moralejo¹,

Gomila

Montesinos³

et al. 2020

Commun Biol

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The recent introductions of the bacterium Xylella fastidiosa (Xf) into Europe are linked to the international plant trade. However, both how and when these entries occurred remains poorly understood. Here, we show how almond scorch leaf disease, which affects ~79% of almond trees in Majorca (Spain) and was previously attributed to fungal pathogens, was in fact triggered by the introduction of Xf around 1993 and subsequently spread to grapevines (Pierceʼs disease). We reconstructed the progression of almond leaf scorch disease by using broad phylogenetic evidence supported by epidemiological data. Bayesian phylogenetic inference predicted that both Xf subspecies found in Majorca, fastidiosa ST1 (95% highest posterior density, HPD: 1990–1997) and multiplex ST81 (95% HPD: 1991–1998), shared their most recent common ancestors with Californian Xf populations associated with almonds and grapevines. Consistent with this chronology, Xf-DNA infections were identified in tree rings dating to 1998. Our findings uncover a previously unknown scenario in Europe and reveal how Pierce’s disease reached the continent.

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“…Xf is an endemic pathogen in America and only recently was identified in southern Italy on olive trees (Saponari et al , 2013), in Corsica and in the south-east Mediterranean coast of France on several hosts (Denancé et al , 2019). Subsequently, records of Xf were reported in Germany on oleander (EPPO, 2016a) and in Spain, Mallorca Island and Andalusia, on different plant species (Landa, 2017; Olmo et al , 2017). Recently, a new finding was also reported in Tuscany (Marchi et al , 2018).…”

Section: Introductionmentioning

confidence: 99%

Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

Faino

Scala

Albanese

et al. 2019

Preprint

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SummaryXylella fastidiosa (Xf) is a polyphagous gram-negative bacterial plant pathogen that can infect more than 300 plant species. It is endemic in America while, in 2013, Xf subsp. pauca was for the first time reported in Europe on olive tree in the Southern Italy. The availability of fast and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf.In this work, we used the Oxford Nanopore Technologies (ONT) device MinION platform for detecting and identifying Xf at species, subspecies and Sequence Type (ST) level straight from infected plant material. The study showed the possibility to detect Xf by direct DNA sequencing and identify the subspecies in highly infected samples. In order to improve sensitivity, Nanopore amplicon sequencing was assessed. Using primers within the set of the seven MLST officially adopted for identifying Xf at type strain level, we developed a workflow consisting in a multiple PCR and an ad hoc pipeline to generate MLST consensus after Nanopore-sequencing of the amplicons. The here-developed combined approach achieved a sensitivity higher than real-time PCR allowing within few hours, the detection and identification of Xf at ST level in infected plant material, also at low level of contamination.Originality Significance StatementIn this work we developed a methodology that allows the detection and identification of Xylella fastidiosa in plant using the Nanopore technology portable device MinION. The approach that we develop resulted more sensitive than methods currently used for detecting X. fastidiosa, like real-time PCR. This approach can be extensively used for X. fastidiosa detection and it may pave the road for the detection of other tedious vascular pathogens.

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Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain IVIA5235, Isolated from Prunus avium in Mallorca Island, Spain

Abstract: We report the complete annotated genome sequence of the plant-pathogenic bacterium Xylella fastidiosa subsp. fastidiosa strain IVIA5235.

Cited by 15 publications

References 8 publications

Insights into the epidemiology of Pierce's disease in vineyards of Mallorca, Spain

Insights into the epidemiology of Pierce's disease in vineyards of Mallorca, Spain

Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe

Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

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