Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp. fuscans Strain CFBP 4884

Article de revue (Article scientifique dans une revue à comité de lecture)International audienceWe report the draft genome sequence of the flagellated strain CFBP 4884 of Xanthomonas fuscans subsp. fuscans, which was isolatedin an outbreak of common bacterial blight of beans along with non-flagellated strains. Comparative genomics will allowone to decipher the genomic diversity of strains cohabiting in epidemics.</p

Classifier systems as 'Animat' architectures for action selection in MMORPG

International audienceClassifier systems (CS) are used as control architectures for simulated animals or robots in order to decide what to do at each time. We will explain why these systems are good candidates for action selection mechanisms of Non Player Characters. After having described different classifier systems, we will introduce a new CS architecture, acting in a multi-agent environment, which is adapted to the specific constraints of the ‘Massively Multi-players Online Role Playing Games’

Clavibacter lycopersici sp. nov.: a peach-colored actinobacterium isolated from symptomless tomato plant

International audienceIn 2015, Gram-positive peach-coloured actinobacterial strains were isolated from symptomless tomato phyllosphere in Iran. Biochemical and physiological characteristics, as well as 16S rRNA phylogeny showed that the strains belong to Clavibacter sp., while they were non-pathogenic on the host of isolation, and morphologically distinct from the tomato pathogen C. michiganensis and other plant-associated bacteria. Multilocus sequence analysis of five housekeeping genes showed that the two peach-coloured strains CFBP 8615 T (Tom532 T ) and CFBP 8616 (Tom495) were phylogenetically distinct from all validly described Clavibacter species. Whole genome sequence-based indices, i.e. average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH), showed that the two peach-colored strains share nearly 100 % orthoANI value with one another, while they differ from all validly described Clavibacter species with the orthoANI/dDDH values &lt;93 % and &lt;50 %, respectively. Thus, based on both phenotypic features and orthoANI/dDDH indices the peach-coloured strains could belong to a new species within Clavibacter . In this study, we provide a formal species description for the peach-coloured tomato-associated Clavibacter strains. Clavibacter lycopersici sp. nov. is proposed for the new species with Tom532 T = CFBP 8615 T = ICMP 22100 T as type strain

Preliminary definitions of ‘flare’ in axial spondyloarthritis, based on pain, BASDAI and ASDAS-CRP: an ASAS initiative

International audienceIntroduction Flares may be used as outcomes in axial spondyloarthritis (axSpA) trials or observational studies. The objective was to develop a definition for ‘flare’ (or worsening) in axSpA, based on validated composite indices, to be used in the context of clinical trial design.Methods (1) Systematic literature review of definitions of ‘flare’ in published randomised controlled trials in axSpA. (2) Vignette exercise: 140 scenarios were constructed for a typical patient with axSpA seen at two consecutive visits. Each scenario included a change in one of the following outcomes: pain, Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), BASDAI plus C-reactive protein (CRP) or Ankylosing Spondylitis Disease Activity Score (ASDAS)-CRP. Each Assessment of Spondyloarthritis (ASAS) expert determined if every scenario from a random sample of 46 scenarios was considered a flare (yes/no). Receiver-operating characteristic (ROC) analyses were applied to derive optimal cut-off values. (3) ASAS consensus was reached.Results (1) The literature review yielded 38 studies using some definition of ‘flare’, with 27 different definitions indicating important heterogeneity. The most frequent definitions were based on BASDAI changes or pain changes. (2) 121 ASAS experts completed 4999 flare assessments. The areas under the ROC curves were high (range: 0.88–0.89). Preliminary cut-offs for pain (N=3), BASDAI (N=5) and ASDAS-CRP (N=4) were chosen, with a range of sensitivity 0.60–0.99 and range of specificity 0.40–0.94 against the expert's opinions.Conclusions This data-driven ASAS consensus process has led to 12 preliminary draft definitions of ‘flare’ in axSpA, based on widely used indices. These preliminary definitions will need validation in real patient data

Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa

International audienceBacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. So far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa as the expected 229 bp DNA fragment was not amplified in the closely-related pathovars nor in other xanthomonads, wheat pathogenic bacteria, and other plant pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/µl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 cfu/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 cfu/g while culture plate method was able to detect the pathogen at a concentration of 50 × 105 cfu/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease

High-Quality Draft Genome Sequence of Curtobacterium sp. Strain Ferrero

International audienceHere, we present the high-quality draft genome sequence of Curtobacterium sp. strain Ferrero, an actinobacterium belonging to a novel species isolated as an environmental contaminant in a bacterial cell culture. The assembled genome of 3,694,888 bp in 49 contigs has a GC content of 71.6% and contains 3,516 predicted gene

Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae , C. flaccumfaciens pv. oortii , and C. flaccumfaciens pv. poinsettiae

International audienceRNA interference is a mechanism of suppressing gene expression in plants, animals and fungi. This regulation mechanism involves three main enzymes, Dicers (Dcr), Argonautes (Ago) and RNA Dependent RNA Polymerases (Rdrp) allowing to produce smallRNAs. RNA interference and smallRNAs have a role in the plant–microorganisms interaction, either in a pathogenic or in a symbiotic relationships. Alternaria brassicicola is a pathogenic fungus of the Brassicaceae plants. During plant infection, it is able to transmit itself vertically and horizontally, giving advantages for new infection and dissemination. To investigate RNA interference and the presence of smallRNAs in A. brassicicola, an in silico analysis was achieved. Two DCR, 4 AGO and 3 RDRP genes were identified comforting the presence of smallRNAs in A. brassicicola. SmallRNA sequencing from wild-type strain and DCR deleted mutants allowed the identifcation of 17 miRNAs in A. brassicicola. The synthesis of these miRNAs is only weakly influenced by the inactivation of DCR genes suggesting the possible existence of an alternative Dicer-independent miRNA synthesis pathway. Target's prediction of A. brassicicola miRNAs identified genes in the fungus and in the plant model Arabidopsis thaliana. Some miRNAs were predicted to target A. thaliana genes involved in the methylation of histone and in the disease resistanc