Complete Circularized Genome Data of Two Spanish strains of <i>Xylella fastidiosa</i> (IVIA5235 and IVIA5901) Using Hybrid Assembly Approaches

Arias-Giraldo, Luis F.; Giampetruzzi, Annalisa; Metsis, Madis; Marco‐Noales, Ester; Imperial, Juan; Velasco-Amo, María Pilar; Román-Écija, Miguel; Landa, Blanca B.

doi:10.1094/phyto-01-20-0012-a

Cited by 10 publications

(10 citation statements)

References 11 publications

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“…multiplex strain RIV5 [23], whose sequence is nearly identical to pXFAS01 from Xf subsp. fastidiosa strain M23 and pXFAS_5235 plasmid present in the Spanish strain IVIA5235 [22].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, all of the genomes obtained from several strains of Xf subsp. fastidiosa ST1 isolated from grapes and almonds in Mallorca revealed the presence of a 38 kb plasmid (pXFAS_5235), with a high sequence similarity to the conjugative plasmid pXFAS01 from isolate M23 of the same subspecies and ST, causing ALSD in California [18,21,22]. Interestingly, a nearly identical plasmid was found in Xf subsp.…”

Section: Introductionmentioning

confidence: 99%

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Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain

Velasco-Amo

Arias-Giraldo

Olivares-García

et al. 2022

Plants

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Xylella fastidiosa (Xf) is a phytopathogenic bacterium with a repertoire of self-replicating genetic elements, including plasmids, pathogenicity islands, and prophages. These elements provide potential avenues for horizontal gene transfer both within and between species and have the ability to confer new virulence traits, including the ability to colonize new host plants. However, they can also serve as a ‘footprint’ to type plasmid-bearing strains. Genome sequencing of several strains of Xf subsp. fastidiosa sequence type (ST) 1 from Mallorca Island, Spain, revealed the presence of a 38 kb plasmid (pXFAS_5235). In this study, we developed a PCR-based typing approach using primers targeting the traC gene to determine the presence of pXFAS_5235 plasmid or other plasmids carrying this gene in a world-wide collection of 65 strains X. fastidiosa from different subspecies and STs or in 226 plant samples naturally infected by the bacterium obtained from the different outbreaks of Xf in Spain. The traC gene was amplified only in the plant samples obtained from Mallorca Island infected by Xf subsp. fastidiosa ST1 and from all Spanish strains belonging to this ST. Maximum-likelihood phylogenetic tree of traC revealed a close relatedness among Spanish and Californian strains carrying similar plasmids. Our results confirm previous studies, which suggested that a single introduction event of Xf subsp. fastidiosa ST1 occurred in the Balearic Islands. Further studies on the presence and role of plasmids in Xf strains belonging to the same or different subspecies and STs can provide important information in studies of epidemiology, ecology, and evolution of this plant pathogen.

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“…multiplex strain RIV5 [23], whose sequence is nearly identical to pXFAS01 from Xf subsp. fastidiosa strain M23 and pXFAS_5235 plasmid present in the Spanish strain IVIA5235 [22].…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain

Velasco-Amo

Arias-Giraldo

Olivares-García

et al. 2022

Plants

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“…The outbreak in Alicante was first reported in June 2017 and Xf subsp. multiplex was identified (Schaad et al 2004;Arias-Giraldo et al 2020;Landa et al 2020). Since then delimiting surveys have been conducted to update the boundaries of the demarcated area and eradication measures have been applied, including the removal of all host plants within the infested zones and vector control.…”

Section: Introductionmentioning

confidence: 99%

Tracking the outbreak: an optimized sequential adaptive strategy for Xylella fastidiosa delimiting surveys

Lázaro

López‐Quílez

et al. 2021

Biol Invasions

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The EU plant health legislation enforces the implementation of intensive surveillance programs for quarantine pests. After an outbreak, surveys are implemented to delimit the extent of the infested zone and to manage disease control. Surveillance in agricultural and natural environments can be enhanced by increasing the survey efforts. Budget constraints often limit inspection and sampling intensities, thus making it necessary to adapt and optimize surveillance strategies. A sequential adaptive delimiting survey involving a three-phase and a two-phase design with increasing spatial resolution was developed and implemented for the Xylella fastidiosa demarcated area in Alicante, Spain. Inspection and sampling intensities were optimized using simulation-based methods. Sampling intensity thresholds were evaluated by quantifying their effect on the estimation of X. fastidiosa incidence. This strategy made it possible to sequence inspection and sampling taking into account increasing spatial resolutions, and to adapt the inspection and sampling intensities according to the information obtained in the previous, coarser, spatial resolution. The proposed strategy was able to efficiently delimit the extent of Xylella fastidiosa, while improving on the efficiency and maintaining the efficacy of the official survey campaign. From a methodological perspective, our approach provides new insights into alternative delimiting designs and new reference sampling intensity values.

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“…Botanical identificationThe botanical identification of the plant, both as reported in the publication and according to the updated taxonomy of the EPPO Global Database5 , is reported in this section Plant EPPO code EPPO code of the plant species, from the EPPO global database 5 . For plant species not present in the EPPO global database, a new code was created in the EFSA catalogue.…”

mentioning

confidence: 99%

“…5 , is reported in this section Plant EPPO code EPPO code of the plant species, from the EPPO global database5 . For plant species not present in the EPPO global database, a new code was created in the EFSA catalogue.…”

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confidence: 99%

Update of the Xylella spp. host plant database – systematic literature search up to 31 December 2020

Delbianco¹,

Gibin²,

Pasinato³

et al. 2021

EFS2

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Following a request from the European Commission, EFSA was asked to create and regularly update a database of host plant species of Xylella spp. Complying with an extension of the previous mandate, which now covers the period 2021-2026, the current version of Xylella spp. host plant database updates the previous release dated April 2020. Informative data have been extracted from 86 recent publications retrieved through an extensive literature search. This report is related to the fourth version of the database published in Zenodo in the EFSA Knowledge Junction community, covering articles selected from: a systematic literature review conducted up to 31 December 2020, Europhyt outbreak notifications up to 18 March 2021 and communications from research groups and national authorities. Forty-three new host plant species of X. fastidiosa, identified through the data extracted from the selected publications, have been added to the database. Those plant species were reported as naturally or artificially infected by subsp. fastidiosa, multiplex, pauca or unknown (i.e. not reported in the publication) subspecies of X. fastidiosa. New information on the tolerant/resistant response of plant species or varieties to X. fastidiosa infection is also reported. No additional data were retrieved for X. taiwanensis. This new version of the database includes no update on the number of Sequence Types (STs) identified so far, which remains unchanged. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between: sequencing, pure culture isolation) reaches now 385 plant species, 179 genera and 67 families. Such numbers rise to 638 plant species, 289 genera and 87 families if considered regardless of the detection method applied. The database will be issued twice per year, with the aim to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp.

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Complete Circularized Genome Data of Two Spanish strains of Xylella fastidiosa (IVIA5235 and IVIA5901) Using Hybrid Assembly Approaches

Cited by 10 publications

References 11 publications

Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain

Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain

Tracking the outbreak: an optimized sequential adaptive strategy for Xylella fastidiosa delimiting surveys

Update of the Xylella spp. host plant database – systematic literature search up to 31 December 2020

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