Pan-genomic analysis permits differentiation of virulent and non-virulent strains of Xanthomonas arboricola that cohabit Prunus spp. and elucidate bacterial virulence factors

Xanthomonas arboricola is a plant-associated bacterial species that causes diseases on several plant hosts. One of the most virulent pathovars within this species is X. arboricola pv. pruni (Xap), the causal agent of bacterial spot disease of stone fruit trees and almond. Recently, a non-virulent Xap-look-a-like strain isolated from Prunus was characterized and its genome compared to pathogenic strains of Xap, revealing differences in the profile of virulence factors, such as the genes related to the type III secretion system (T3SS) and type III effectors (T3Es). The existence of this atypical strain arouses several questions associated with the abundance, the pathogenicity, and the evolutionary context of X. arboricola on Prunus hosts. After an initial characterization of a collection of Xanthomonas strains isolated from Prunus bacterial spot outbreaks in Spain during the past decade, six Xap-look-a-like strains, that did not clustered with the pathogenic strains of Xap according to a multi locus sequence analysis, were identified. Pathogenicity of these strains was analyzed and the genome sequences of two Xap-look-a-like strains, CITA 14 and CITA 124, non-virulent to Prunus spp., were obtained and compared to those available genomes of X. arboricola associated with this host plant. Differences were found among the genomes of the virulent and the Prunus non-virulent strains in several characters related to the pathogenesis process. Additionally, a pan-genomic analysis that included the available genomes of X. arboricola, revealed that the atypical strains associated with Prunus were related to a group of non-virulent or low virulent strains isolated from a wide host range. The repertoire of the genes related to T3SS and T3Es varied among the strains of this cluster and those strains related to the most virulent pathovars of the species, corylina, juglandis, and pruni. This variability provides information about the potential evolutionary process associated to the acquisition of pathogenicity and host specificity in X. arboricola. Finally, based in the genomic differences observed between the virulent and the non-virulent strains isolated from Prunus, a sensitive and specific real-time PCR protocol was designed to detect and identify Xap strains. This method avoids miss-identifications due to atypical strains of X. arboricola that can cohabit Prunus

Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain

Xanthomonas arboricola is a species in genus Xanthomonas which is mainly comprised of plant pathogens. Among the members of this taxon, X. arboricola pv. pruni, the causal agent of bacterial spot disease of stone fruits and almond, is distributed worldwide although it is considered a quarantine pathogen in the European Union. Herein, we report the draft genome sequence, the classification, the annotation and the sequence analyses of a virulent strain, IVIA 2626.1, and an avirulent strain, CITA 44, of X. arboricola associated with Prunus spp. The draft genome sequence of IVIA 2626.1 consists of 5, 027, 671 bp, 4, 720 protein coding genes and 50 RNA encoding genes. The draft genome sequence of strain CITA 44 consists of 4, 760, 482 bp, 4, 250 protein coding genes and 56 RNA coding genes. Initial comparative analyses reveals differences in the presence of structural and regulatory components of the type IV pilus, the type III secretion system, the type III effectors as well as variations in the number of the type IV secretion systems. The genome sequence data for these strains will facilitate the development of molecular diagnostics protocols that differentiate virulent and avirulent strains. In addition, comparative genome analysis will provide insights into the plant-pathogen interaction during the bacterial spot disease process

Criteria for efficient prevention of dissemination and successful eradication of Erwinia amylovora (the cause of fire blight) in Aragon, Spain

Erwinia amylovora was detected on pome fruits in the Aragon region (North-Eastern Spain), in a ca. 5 km radius area located in the mid Jalon river (mid Ebro Valley) in the province of Zaragoza, during 2000-2003. Eight years have now passed since this pathogen was last detected, without new infections being reported in the same area. The bases for surveys and rapid eradication performed have been analyzed in detail to understand the reasons for the success in removing fireblight. The results demonstrate that intensive surveillance, risk assessment, plant analyses using accurate identification methods, and, especially, rapid total or selective eradication of infected trees in the plots have been very effective in preventing the generalized spread of fireblight and in delaying economic losses associated with this disease. Eradication and compensation to growers, estimated to cost approx. (sic) 467,000, were clearly counterbalanced by the economic value of apple and pear production in the 2000-2003 period (approx. (sic) 368 million). Fire blight risk-assessment, using the MARYBLYT system, showed that climatic conditions in the studied area were favourable to infections during the analyzed period (1997-2006). Molecular characterization of E. amylovora strains had revealed their homogeneity, suggesting that these fire blight episodes could have been caused by just one inoculum source, supporting the hypothesis that there was a unique introduction of E. amylovora in the studied area. Spatial spread of E. amylovora to trees was analyzed within six orchards, indicating an aggregated distribution model. This Spanish experience demonstrates the success of scientifically-based prevention methods that lead to the deployment of a fast and strict containment strategy, useful for other Mediterranean areas

Criteria for efficient prevention of dissemination and successful eradication of Erwinia amylovora (the cause of fire blight) in Aragon, Spain

Erwinia amylovora was detected on pome fruits in the Aragon region (North-Eastern Spain), in a ca. 5 km radius area located in the mid Jalon river (mid Ebro Valley) in the province of Zaragoza, during 2000-2003. Eight years have now passed since this pathogen was last detected, without new infections being reported in the same area. The bases for surveys and rapid eradication performed have been analyzed in detail to understand the reasons for the success in removing fireblight. The results demonstrate that intensive surveillance, risk assessment, plant analyses using accurate identification methods, and, especially, rapid total or selective eradication of infected trees in the plots have been very effective in preventing the generalized spread of fireblight and in delaying economic losses associated with this disease. Eradication and compensation to growers, estimated to cost approx. (sic) 467,000, were clearly counterbalanced by the economic value of apple and pear production in the 2000-2003 period (approx. (sic) 368 million). Fire blight risk-assessment, using the MARYBLYT system, showed that climatic conditions in the studied area were favourable to infections during the analyzed period (1997-2006). Molecular characterization of E. amylovora strains had revealed their homogeneity, suggesting that these fire blight episodes could have been caused by just one inoculum source, supporting the hypothesis that there was a unique introduction of E. amylovora in the studied area. Spatial spread of E. amylovora to trees was analyzed within six orchards, indicating an aggregated distribution model. This Spanish experience demonstrates the success of scientifically-based prevention methods that lead to the deployment of a fast and strict containment strategy, useful for other Mediterranean areas

Multilocus variable number of tandem repeat analysis reveals multiple introductions in Spain of Xanthomonas arboricola pv. Pruni, the causal agent of bacterial spot disease of stone fruits and almond

Xanthomonas arboricola pv. pruni is the causal agent of the bacterial spot disease of stone fruits, almond and some ornamental Prunus species. In Spain it was first detected in 2002 and since then, several outbreaks have occurred in different regions affecting mainly Japanese plum, peach and almond, both in commercial orchards and nurseries. As the origin of the introduction(s) was unknown, we have assessed the genetic diversity of 239 X. arboricola pv. pruni strains collected from 11 Spanish provinces from 2002 to 2013 and 25 reference strains from international collections. We have developed an optimized multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 18 microsatellites and five minisatellites. A high discriminatory power was achieved since almost 50% of the Spanish strains were distinguishable, confirming the usefulness of this genotyping technique at small spatio-temporal scales. Spanish strains grouped in 18 genetic clusters (conservatively delineated so that each cluster contained haplotype networks linked by up to quadruple-locus variations). Furthermore, pairwise comparisons among populations from different provinces showed a strong genetic differentiation. Our results suggest multiple introductions of this pathogen in Spain and redistribution through contaminated nursery propagative plant material

Estado fitosanitario del azafrán en Aragón (España): Insectos, ácaros, nematodos, virus, bacterias y malas hierbas

El azafrán cultivado en España está adquiriendo relevancia en las últimas décadas como producto de gran calidad, lo que requiere la selección de cormos, sus órganos reproductivos, sanos para la plantación con el objetivo de mantener un adecuado estado fitosanitario del cultivo. Este trabajo presenta un estudio del estado fitosanitario del azafrán en Teruel, donde el cultivo fue muy importante económica y socialmente. Además, este estudio pretende ser de utilidad para las zonas productoras con características agroclimáticas similares. Con dichos objetivos, se prospectaron 10 plantaciones comerciales de azafrán en 6 localidades del valle del Jiloca entre los años 2008 y 2011, estudiando la presencia de insectos, ácaros, nematodos, virus, bacterias y malas hierbas. El ácaro Rhizoglyphus robini, una de las plagas más importantes del azafrán, se detectó en los cormos y en el suelo en una parcela. También el nematodo Aphelenchoides blastophtorus, plaga en plantas ornamentales, se encontró abundantemente en cormos de dos parcelas. Se detectaron infecciones ocasionales de virus del género potyvirus en el cultivo y en la mala hierba Eruca vesicaria. Las malas hierbas Lolium rigidum y Descurainia sophia podrían causar serios problemas de competencia al cultivo y se considera necesario realizar operaciones de escarda en otoño y en invierno. No se detectaron insectos nocivos ni bacterias fitopatógenas. La multiplicación vegetativa del azafrán hace aconsejable realizar muestreos, especialmente en los cormos antes de ser replantados, para detectar la presencia de ácaros, nematodos y virus que podrían ocasionar pérdidas de producción y calidad. In the last decades, saffron produced in Spain is gaining relevance as a high-quality product, which requires the selection of healthy corms (the reproductive organ) for planting in order to maintain adequa-te phytosanitary status of the crop. In this work, the phytosanitary status of saffron was studied in Teruel (Aragón, Spain), where the crop has economic and social importance. Moreover, it aims to be useful for the production areas with similar agro-climatic characteristics. Ten commercial saffron plantations in six locations of the Jiloca valley have been surveyed between 2008 and 2011 and the presence of insects, mites, nematodes, virus, bacteria and weeds was studied. The mite Rhizoglyphus robini, one of the most important pests of saffron, was detected in both corms and soil in one plantation. The nematode Aphelenchoides blastophtorus, pest in ornamental plants, was also found in corms in two plantations. Potyvirus infections were occasionally detected in both the crop and in the weed Eruca vesicaria. The weeds Lolium rigidum and Descurainia sophia could cause diminutions of the yield by competition, therefore, weeding operations are necessary in autumn and winter. No harmful insects and phytopatogenic bacteria were detected. Because reproduction is only possible through corm propagation, it is advisable to analyse the plants, especially the corms, before being re-planted, in order to detect the presence of mites, nematodes and virus that could reduce yield and quality decreases

Primera detección de Lonsdalea quercina subsp. populi en chopo en España

Lonsdalea quercina (ex Brenneria quercina) subsp. populi es una bacteria recientemente identificada en Hungría y China como una nueva subespecie causante del chancro de la corteza del chopo. Los árboles afectados presentan chancros longitudinales en el tronco, de los que fluyen abundantes exudados espumosos de color blanco y exudados acuosos oscuros que tiñen la corteza. Los chopos afectados muestran un debilitamiento generalizado. En España se han localizado choperas con síntomas similares y se ha identificado L. quercina subsp. populi como el agente causal de los mismos. En este trabajo se presenta la primera detección de esta bacteria en España y se describen los métodos de diagnóstico e identificación utilizados. Esta nueva bacteriosis podría tener un impacto económico importante, siendo necesario evaluar las pérdidas causadas y realizar nuevas prospecciones para determinar su distribución en el país