Complete genome sequence of Pseudomonas viridiflava CFBP 1590: isolated from diseased cherry in France

Pseudomonas viridiflava causes foliar and stem necrosis, as well as stem and root rot on a wide range of plants. We report here the first complete genome of a P. viridiflava strain, isolated from diseased tissue of a cherry tree

High-quality draft genome sequence of xanthomonas arboricola pv. juglandis CPBF 1521, isolated from leaves of a symptomatic walnut tree in Portugal without a past of phytosanitary treatment

Here, we report the draft genome sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, isolated from symptomatic leaves of an ornamental walnut in a public site in Portugal without any record of phytosanitary treatment. This isolate may constitute a genomic reference of a wild-type strain in comparative genomics studies

High-Quality draft genome sequence of xanthomonas sp. strain CPBF 424, a walnut-pathogenic strain with atypical features

We report here the draft genome sequence of Xanthomonas sp. strain CPBF 424, isolated from a diseased walnut tree. Multilocus sequence analysis showed that this walnut-pathogenic isolate is located between the nonpathogenic X. arboricola and X. prunicola clusters. These features make this strain a promising reference to disclose new genetic determinants of pathogenesis

Complete genome sequence data of two Xanthomonas arboricola strains isolated from blueberry plants displaying bacterial leaf blight in Poland

We report here the complete genome sequences of two Xanthomonas arboricola strains isolated in 2013 from blueberry plants displaying bacterial leaf blight in Poland. These two strains – the new blueberry pathogens – were sequenced using a hybrid approach with short- and long-read technologies. The genomes will be used for further analysis of evolution within the species X. arboricola for determining if the strains constitute a new pathovar within the species and improving the molecular diagnostics of this relevant pathogen of blueberry

Erwinia species identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry

Rapid and reliable identification of plant pathogenic bacteria is critical for effective implementation of phytosanitary measures. The genus Erwinia includes a number of economically important plant pathogens such as fire blight agent Erwinia amylovora or Asian pear pathogen Erwinia pyrifoliae, together with closely related plant epiphytes of unknown pathogenicity or even with a potential use for biological control like Erwinia tasmaniensis or Erwinia billingiae, respectively. Current laboratory methods to achieve satisfactory identification and discrimination between species within the Erwinia genus are based on the isolation on semi-selective media, serology, specific PCR and gene locus sequencing: these approaches are complicated and time-consuming, often requiring a priori assumptions over the identity of the isolates. Here we present a streamlined approach based on whole-cell Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS) based on the AXIMA mass spectrometer of Shimadzu-Biotech Corp that demonstrates the potential of this technology for quick species identification in plant diagnostics within the genus Erwinia

Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants

Xanthomonas fragariae is a worldwide spread plant bacterial disease causing angular leaf spots, and thus reducing the yield of production for strawberry fruits. Three isolates with variable geographic and time origins were sequenced with long-read technology (PacBio) to generate finished genomes of virulent strains and observe their variability in content

Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization

Sprouted seeds represent a great risk for infection by human enteric pathogens because of favourable growth conditions for pathogens during their germination. The aim of this study was to identify mechanisms of interactions of Salmonella enterica subsp. enterica Weltevreden with alfalfa sprouts. RNA-seq analysis of S. Weltevreden grown with sprouts in comparison with M9-glucose medium showed that among a total of 4158 annotated coding sequences, 177 genes (4.3%) and 345 genes (8.3%) were transcribed at higher levels with sprouts and in minimal medium respectively. Genes that were higher transcribed with sprouts are coding for proteins involved in mechanisms known to be important for attachment, motility and biofilm formation. Besides gene expression required for phenotypic adaption, genes involved in sulphate acquisition were higher transcribed, suggesting that the surface on alfalfa sprouts may be poor in sulphate. Genes encoding structural and effector proteins of Salmonella pathogenicity island 2, involved in survival within macrophages during infection of animal tissue, were higher transcribed with sprouts possibly as a response to environmental conditions. This study provides insight on additional mechanisms that may be important for pathogen interactions with sprouts

High-quality draft genome sequences of five xanthomonas arboricola pv. fragariae isolates

Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight. We report here the first draft whole-genome sequences of fiveX. arboricolapv. fragariae isolates from Italy and France

Complete genome sequences of erwinia amylovora phages vB_EamP-S2 and vB_EamM-Bue1

Phages vB_EamP-S2 (S2) and vB_EamM-Bue1 (Bue1) infect the plant pathogen Erwinia amylovora. S2 has a genome size of 45,495 bp and belongs to the genus SP6virus. The genome size of Bue1, related to Salmonella phage Vil, is 164,037 bp. Both phages possess a depolymerase enzyme, a frequent feature of E. amylovora phages

Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description

Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen