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5. Complete and Circularized Genome Sequences of Three Xanthomonas Strains Pathogenic on Soybean and Alfalfa

Author

Ruh, Mylène, Briand, Martial, Bonneau, Sophie, Darrasse, Armelle, JACQUES, Marie-Agnès, Chen, Nicolas W. G., Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
fungi, food and beverages, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract

International audience; We report the complete and circularized genome sequences of two strains of Xanthomonas citri pv. glycines causing bacterial pustule on soybean and one strain of Xanthomonas euvesicatoria pv. alfalfae causing bacterial leaf and stem spot on alfalfa. These assemblies provide high-quality material for functional and evolutionary studies of these legume pathogens.

Published
2021
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6. The peptidyl-prolyl isomerase motif is lacking in PmpA, the PrsA-like protein involved in the secretion machinery of Lactococcus lactis

Author

Drouault, Sophie, Anba, Jamila, Bonneau, Sophie, Bolotin, Alexander, Ehrlich, S. Dusko, and Renault, Pierre

Subjects
Microbiological research -- Analysis, Microbiology -- Environmental aspects, Isomerases -- Genetic aspects, Protein folding -- Genetic aspects, Secretion -- Genetic aspects, Lactococcus -- Genetic aspects, Bacterial proteins -- Genetic aspects, Gene expression -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on Lactococcus lactis IL-1403. The characterization of the gene which chromosomically encodes PrsA-like protein has been carried out and the results demonstrate that this gene encodes a lipoprotein involved in L. lactis secretion machinery

Published
2002

7. Genetic characterization of the major lactococcal aromatic aminotransferase and its involvement in conversion of amino acids to aroma compounds

Author

Rijnen, Liesbeth, Bonneau, Sophie, and Yvon, Mireille

Subjects
Microbiological research -- Analysis, Amino acids -- Research, Aromatic compounds -- Research, Biosynthesis -- Physiological aspects, Biological sciences
Abstract

Research conducted on the role of aromatic aminotransferase (AraT) in amino acid biosynthesis and amino acid conversion to aroma compounds is presented. Results indicate that AraT is responsible for the aromatic amino acid degradation.

Published
1999

9. Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen

Author

Ferreira, Marisa A. S. V., primary, Bonneau, Sophie, additional, Briand, Martial, additional, Cesbron, Sophie, additional, Portier, Perrine, additional, Darrasse, Armelle, additional, Gama, Marco A. S., additional, Barbosa, Maria Angélica G., additional, Mariano, Rosa de L. R., additional, Souza, Elineide B., additional, and Jacques, Marie-Agnès, additional

Published
2019
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12. Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean

Author

Chen, Nicolas W.G., Serres-Giardi, Laurana, Ruh, Mylène, Briand, Martial, Bonneau, Sophie, Darrasse, Armelle, Barbe, Valérie, Gagnevin, Lionel, Koebnik, Ralf, Jacques, Marie Agnès, Chen, Nicolas W.G., Serres-Giardi, Laurana, Ruh, Mylène, Briand, Martial, Bonneau, Sophie, Darrasse, Armelle, Barbe, Valérie, Gagnevin, Lionel, Koebnik, Ralf, and Jacques, Marie Agnès

Abstract

Background: Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean. Results: To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight. Conclusions: Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers.

Published
2018

13. Additional file 7: Figure S3. of Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors

Author

MylèNe Ruh, Briand, Martial, Bonneau, Sophie, Marie-AgnèS Jacques, and Chen, Nicolas

Abstract

Phylogenetic trees of N-ter and C-ter-encoding regions of tal genes with sequences published by Aritua et al. (2015). Bootstrap values greater than 50% (100 replicates) are shown and horizontal scale bars represent the number of nucleotide substitutions per site. The tal genes from the X. citri pv. fuscans genetic lineages fuscans, NF2 and NF3 are indicated in red, X. phaseoli pv. phaseoli NF1 lineage in blue, X. citri pv. aurantifolii in pink and X. phaseoli pv. manihotis in purple. The sequences published by Aritua et al. (2015) are in bold. Both ML trees were constructed using tal genes from X. translucens pv. undulosa XT4699 as outgroups. a ML tree constructed on a nucleotide alignment of the N-ter-encoding region of tal genes. b ML tree constructed on a nucleotide alignment of the C-ter-encoding region of tal genes. (PPTX 137 kb)

Published
2017
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14. Additional file 3: Figure S1. of Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors

Author

Ruh, Mylène, Briand, Martial, Bonneau, Sophie, Marie-Agnès Jacques, and Chen, Nicolas

Abstract

Gel photograph showing the sizes obtained for tal23A_CFBP4885 (Xfutal1) and tal18H_CFBP4885 (Xfutal2) after PCR amplification. Amplification was performed using XapF2 and XapR primers on plasmidic DNA from the CFBP4885 strain (Additional file 18: Table S11). Expected PCR product sizes for tal23A_CFBP4885 and tal18H_CFBP4885 were 4604 bp and 3074 bp for Sanger sequencing of the entire genome, respectively, and 3686 bp and 3176 bp for SMRT sequencing of the entire genome, respectively. (DOCX 2788 kb)

Published
2017
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16. Additional file 8: Figure S4. of Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors

Author

MylèNe Ruh, Briand, Martial, Bonneau, Sophie, Marie-AgnèS Jacques, and Chen, Nicolas

Subjects
education
Abstract

Circular representation of plasmids A and C. Genomic sequences were compared and converted in a graphical map using CGView (Grant et al., 2012) with strain CFBP4885 as reference. Colours differ according to identity percentage (see legend). Strains order, ANIb and alignment percentages are indicated in the center of each graphical map. Localisation of tal genes are highlighted by green zones. Absence of tal genes in plasmid A from strains CFBP6164 and CFBP6546R is indicated by a black cross. (PDF 444 kb)

Published
2017
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17. Additional file 19: Figure S8. of Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors

Author

MylèNe Ruh, Briand, Martial, Bonneau, Sophie, Marie-AgnèS Jacques, and Chen, Nicolas

Abstract

Phylogenetic trees of N-ter- and C-ter-encoding regions of tal genes used for the Kishino-Hasegawa-Templeton test. Bootstrap values greater than 50% are shown for 1000 replicates and horizontal scale bars represent the number of nucleotide substitutions per site. a ML tree constructed on a nucleotide alignment of the N-ter-encoding region of tal genes from X. citri pv. fuscans, X. citri pv. aurantifolii, X. phaseoli pv. phaseoli and X. phaseoli pv. manihotis strains using a tal gene from X. translucens pv. undulosa XT4699 as outgroup. b ML tree constructed on a nucleotide alignment of the C-ter-encoding region of tal genes from X. citri pv. fuscans, X. citri pv. aurantifolii, X. phaseoli pv. phaseoli and X. phaseoli pv. manihotis strains using a tal gene from X. translucens pv. undulosa XT4699 as outgroup. (PPTX 56 kb)

Published
2017
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21. Recombination-prone bacterial strains form a reservoir from which epidemic clones emerge in agroecosystems

Author

MERDA, Déborah, Bonneau, Sophie, GUIMBAUD, Jean-François, Durand, Karine, Brin, Chrystelle, Boureau, Tristan, Lemaire, Christophe, Jacques, Marie Agnes, Le Saux, Marion, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

The acquisition of virulence-related genes through horizontal gene transfer can modify the pathogenic profiles of strains and lead to the emergence of new diseases. Xanthomonas arboricola is a bacterial species largely known for the damage it causes to stone and nut fruit trees worldwide. In addition to these host-specific populations called pathovars, many nonpathogenic strains have been identified in this species. Their evolutionary significance in the context of pathogen emergence is unknown. We looked at seven housekeeping genes amplified from 187 pathogenic and nonpathogenic strains isolated from various plants worldwide to analyze population genetics and recombination dynamics. We also examined the dynamics of the gains and losses of genes associated with life history traits (LHTs) during X. arboricola evolution. We discovered that X. arboricola presents an epidemic population structure. Successful pathovars of trees (i.e., pruni, corylina, and juglandis) are epidemic clones whose emergence appears to be linked to the acquisition of eight genes coding for Type III effectors. The other strains of this species are part of a recombinant network, within which LHT-associated genes might have been lost. We suggest that nonpathogenic strains, because of their high genetic diversity and propensity for recombination, may promote the emergence of pathogenic strains.

Published
2016
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22. Terroir is a key driver of seed-associated microbial assemblages

Author

Klaedtke, Stéphanie, Jacques, Marie Agnes, Raggi, Lorenzo, Preveaux, Anne, Bonneau, Sophie, NEGRI, Valeria, Chable, Véronique, Barret, Matthieu, SAD Paysage (SAD Paysage), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia (UNIPG), Grants awarded by the Region des Pays de la Loire (Qualisem, metaSEED, 2013 10080), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, food and beverages, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces.

Published
2016
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25. Dynamique de la structure du microbiote des semences lors de la germination-levée

Author

Barret, Matthieu, Briand, Martial, Bonneau, Sophie, Préveaux, Anne, Valière, Sophie, Bouchez, Olivier, Simoneau, Philippe, Jacques, Marie-Agnès, Univ Angers, Okina, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
[SDV] Life Sciences [q-bio], [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV]Life Sciences [q-bio], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding
Published
2015

26. Structure and function of the seed microbiota

Author

Campion, Claire, Simoneau, Philippe, Jacques, Marie-Agnès, Barret, Matthieu, Klaedtke, Stephanie, Rezki, Samir, Briand, Martial, Bonneau, Sophie, Préveaux, Anne, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SAD Paysage (SAD Paysage), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université d'Angers (UA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université d'Angers (UA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV]Life Sciences [q-bio], [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Published
2015

27. Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms

Author

Rezki, Samir, primary, Campion, Claire, additional, Iacomi-Vasilescu, Beatrice, additional, Preveaux, Anne, additional, Toualbia, Youness, additional, Bonneau, Sophie, additional, Briand, Martial, additional, Laurent, Emmanuelle, additional, Hunault, Gilles, additional, Simoneau, Philippe, additional, Jacques, Marie-Agnès, additional, and Barret, Matthieu, additional

Published
2016
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28. Genome sequencing of Xanthomonas axonopodis pv. phaseoli CFBP4834-R reveals that flagellar motility is not a general feature of xanthomonads. [Abstract]

Author

Darrasse, Armelle, Carrere, Sébastien, Barbe, Valérie, Bourreau, Tristan, Bernal, Adriana, Bonneau, Sophie, Brin, Chrystelle, Cociancich, Stéphane, Durand, Karine, Fouteau, Stéphanie, Gagnevin, Lionel, Gouzy, Jerome, Guérin, Fabien, Guy, Endrick, Indiana, Arnaud, Koebnik, Ralf, Lauber, Emmanuelle, Munoz, Alejandra, Noel, Laurent D., Pieretti, Isabelle, Poussier, Stéphane, Pruvost, Olivier, Robene-Soustrade, Isabelle, Rott, Philippe, Royer, Monique, Szurek, Boris, van Sluys, Marie-Anne, Verdier, Valérie, Vernière, Christian, Arlat, Mathieu, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universidad de Los Andes [Venezuela] (ULA), Pathologie Végétale (PaVé), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Institut de Recherche pour le Développement (IRD), Résistance des plantes aux bio-agresseurs (UMR RPB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Manceau, Charles and Jacques, Marie-Agnès and Arlat, Mathieu and Lauber, Emmanuelle and Noel, Laurent D. and Gagnevin, Lionel and Pruvost, Olivier and Rott, Philippe and Royer, Monique and Koebnik, Ralf and Verdier, Valérie, Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Universidad de Los Andes [Mérida, Venezuela] (ULA), and Université de Toulouse (UT)

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract

International audience; Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap and filament) are absent in the genome of strain 4834-R that is not motile. Primers were designed to detect this deletion by PCR in a collection of more than 300 strains representing different species and pathovars of Xanthomonas, and less than 5% of the tested xanthomonads strains were found nonmotile because of a deletion in the flagellum gene cluster. We observed that half of the Xapf strains isolated from the same epidemic than strain 4834-R was non-motile and that this ratio was conserved in the strains colonizing the next bean seed generation. Isolation of such variants in a natural epidemic reveals that either flagellar motility is not a key function for fitness or that some complementation occurs within the bacterial population. (Résumé d'auteur)

Published
2012

29. Genome sequencing of Xanthomonas axonopodis pv. phaseoli CFBP4834-R reveals that flagellar motility is not a general feature of xanthomonads

Author

Darrasse, Armelle, Carrère, Sébastien, Barbe, Valérie, Bourreau, Tristan, Bernal, Adriana, Bonneau, Sophie, Brin, Christelle, Cociancich, Stéphane, Durand, Karine, Fouteau, Stéphanie, Gagnevin, Lionel, Gouzy, Jérôme, Guérin, Fabien, Guy, Endrick, Indiana, Arnaud, Koebnik, Ralf, Lauber, Emmanuelle, Munoz, Alejandra, Noel, Laurent D., Pieretti, Isabelle, Poussier, Stéphane, Pruvost, Olivier, Robène-Soustrade, Isabelle, Rott, Philippe, Royer, Monique, Szurek, Boris, Van Sluys, Marie-Anne, Verdier, Valérie, Vernière, Christian, Arlat, Mathieu, Manceau, Charles, and Jacques, Marie Agnès

Subjects
H20 - Maladies des plantes
Abstract

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap and filament) are absent in the genome of strain 4834-R that is not motile. Primers were designed to detect this deletion by PCR in a collection of more than 300 strains representing different species and pathovars of Xanthomonas, and less than 5% of the tested xanthomonads strains were found nonmotile because of a deletion in the flagellum gene cluster. We observed that half of the Xapf strains isolated from the same epidemic than strain 4834-R was non-motile and that this ratio was conserved in the strains colonizing the next bean seed generation. Isolation of such variants in a natural epidemic reveals that either flagellar motility is not a key function for fitness or that some complementation occurs within the bacterial population.

Published
2012

30. Evidences for selection on promoter region reveal a hidden aspect of the multifaceted evolution of the type three effector Avrbs2 in the Xanthomonas axonopodis species

Author

David, P., Hajri, Ahmed, Rousseau, C, Brin, Chrystelle, Bonneau, Sophie, Darrasse, Armelle, Jacques, Marie-Agnès, Bernal, A., Koebnik, Ralf, Hunault, G., Poussier, Stéphane, Lemaire, Christophe, Boureau, Tristan, Pathologie Végétale (PaVé), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Résistance des plantes aux bio-agresseurs (UMR RPB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR)

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2011

36. Emergence Shapes the Structure of the Seed Microbiota

Author

Barret, Matthieu, primary, Briand, Martial, additional, Bonneau, Sophie, additional, Préveaux, Anne, additional, Valière, Sophie, additional, Bouchez, Olivier, additional, Hunault, Gilles, additional, Simoneau, Philippe, additional, and Jacques, Marie-Agnès, additional

Published
2015
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38. Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Author

Darrasse, Armelle, Carrère, Sébastien, Barbe, Valérie, Boureau, Tristan, Arrieta-Ortiz, Mario L., Bonneau, Sophie, Briand, Martial, Brin, Christelle, Cociancich, Stéphane, Durand, Karine, Fouteau, Stéphanie, Gagnevin, Lionel, Guérin, Fabien, Guy, Endrick, Indiana, Arnaud, Koebnik, Ralf, Lauber, Emmanuelle, Munoz, Alejandra, Noel, Laurent D., Pieretti, Isabelle, Poussier, Stéphane, Pruvost, Olivier, Robène-Soustrade, Isabelle, Rott, Philippe, Royer, Monique, Serres-Giardi, Laurana, Szurek, Boris, Van Sluys, Marie-Anne, Verdier, Valérie, Vernière, Christian, Arlat, Mathieu, Manceau, Charles, Jacques, Marie Agnès, Darrasse, Armelle, Carrère, Sébastien, Barbe, Valérie, Boureau, Tristan, Arrieta-Ortiz, Mario L., Bonneau, Sophie, Briand, Martial, Brin, Christelle, Cociancich, Stéphane, Durand, Karine, Fouteau, Stéphanie, Gagnevin, Lionel, Guérin, Fabien, Guy, Endrick, Indiana, Arnaud, Koebnik, Ralf, Lauber, Emmanuelle, Munoz, Alejandra, Noel, Laurent D., Pieretti, Isabelle, Poussier, Stéphane, Pruvost, Olivier, Robène-Soustrade, Isabelle, Rott, Philippe, Royer, Monique, Serres-Giardi, Laurana, Szurek, Boris, Van Sluys, Marie-Anne, Verdier, Valérie, Vernière, Christian, Arlat, Mathieu, Manceau, Charles, and Jacques, Marie Agnès

Abstract

Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

Published
2013

39. Genome sequence of Xanthomonas fuscans subsp. fuscansstrain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Author

Darrasse, Armelle, primary, Carrère, Sébastien, additional, Barbe, Valérie, additional, Boureau, Tristan, additional, Arrieta-Ortiz, Mario L, additional, Bonneau, Sophie, additional, Briand, Martial, additional, Brin, Chrystelle, additional, Cociancich, Stéphane, additional, Durand, Karine, additional, Fouteau, Stéphanie, additional, Gagnevin, Lionel, additional, Guérin, Fabien, additional, Guy, Endrick, additional, Indiana, Arnaud, additional, Koebnik, Ralf, additional, Lauber, Emmanuelle, additional, Munoz, Alejandra, additional, Noël, Laurent D, additional, Pieretti, Isabelle, additional, Poussier, Stéphane, additional, Pruvost, Olivier, additional, Robène-Soustrade, Isabelle, additional, Rott, Philippe, additional, Royer, Monique, additional, Serres-Giardi, Laurana, additional, Szurek, Boris, additional, van Sluys, Marie-Anne, additional, Verdier, Valérie, additional, Vernière, Christian, additional, Arlat, Matthieu, additional, Manceau, Charles, additional, and Jacques, Marie-Agnès, additional

Published
2013
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40. Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

Author

Jacques, Marie-Agnès, primary, Durand, Karine, additional, Orgeur, Geoffrey, additional, Balidas, Samuel, additional, Fricot, Céline, additional, Bonneau, Sophie, additional, Quillévéré, Anne, additional, Audusseau, Corinne, additional, Olivier, Valérie, additional, Grimault, Valérie, additional, and Mathis, René, additional

Published
2012
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42. Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots

Author

Universidad de San Pablo-CEU, National Institutes of Health (US), Rojas Mendoza, Ana M., García de los Ríos, José Esteban, Fischer-Le Saux, Marion, Jiménez Granero, Pedro, Reche, Paloma, Bonneau, Sophie, Sutra, Laurent, Mathieu-Daude, Françoise, McClelland, Michael, Universidad de San Pablo-CEU, National Institutes of Health (US), Rojas Mendoza, Ana M., García de los Ríos, José Esteban, Fischer-Le Saux, Marion, Jiménez Granero, Pedro, Reche, Paloma, Bonneau, Sophie, Sutra, Laurent, Mathieu-Daude, Françoise, and McClelland, Michael

Abstract

Gram-negative bacteria were isolated from knots induced by Pseudomonas savastanoi in olive trees (Olea europaea L.). A total of nine endophytic bacterial strains were isolated, each from inside a different tree knot. Biochemical characterization indicated that all the strains belong to the family Enterobacteriaceae. Phylogenetic analyses of the 16S rRNA genes of these novel isolates revealed that they formed a homogeneous cluster within Erwinia species. DNA signatures of these isolates were identical to those described for the genus Erwinia. The strains formed a homogeneous group as shown by DNA–DNA hybridization analysis and numerical analysis of phenotypic data, clearly differentiated from all species of Erwinia with validly published names. The data provide strong evidence of the differentiation of these strains from the most closely related species. Therefore, these isolates represent a novel species, for which the name Erwinia toletana sp. nov. is proposed. The isolates are available at CFBP, CECT and ATCC. The G+C content is 52±0·5 mol%. The type strain is CFBP 6631T (=A37T=ATCC 700880T=CECT 5263T).

Published
2004

43. Etude du polymorphisme du gene de la caseine Kappa au niveau ADN, chez les bovins

Author

Bonneau, Sophie, Unité de recherche Génétique Biochimique et Cytogénétique (LGBC), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], TECHNIQUE RFLP
Abstract

*INRA, Unite Centrale de Documentation, Jouy-en-Josas (FRA) Diffusion du document : INRA, Unite Centrale de Documentation, Jouy-en-Josas (FRA) Diplôme : BTS

Published
1991

44. Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov.

Author

Mantelin, Sophie, primary, Saux, Marion Fischer-Le, additional, Zakhia, Frédéric, additional, Béna, Gilles, additional, Bonneau, Sophie, additional, Jeder, Habib, additional, de Lajudie, Philippe, additional, and Cleyet-Marel, Jean-Claude, additional

Published
2006
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46. DESSERT.

Author

Bonneau, Sophie

Published
2018

48. Complete and Circularized Genome Sequences of Three Xanthomonas Strains Pathogenic on Soybean and Alfalfa.

Author

Ruh M, Briand M, Bonneau S, Darrasse A, Jacques MA, and Chen NWG

Abstract

We report the complete and circularized genome sequences of two strains of Xanthomonas citri pv. glycines causing bacterial pustule on soybean and one strain of Xanthomonas euvesicatoria pv. alfalfae causing bacterial leaf and stem spot on alfalfa. These assemblies provide high-quality material for functional and evolutionary studies of these legume pathogens.

Published
2021
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