1. Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels
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Isabelle Pieretti, Valérie Verdier, Boris Szurek, Philippe Rott, Monique Royer, Dean W. Gabriel, Charles Manceau, Armelle Darrasse, Ralf Koebnik, Matthieu Arlat, Béatrice Segurens, Valérie Barbe, Stéphane Cociancich, Sophie Mangenot, Marie-Agnès Jacques, Jérôme Gouzy, Arnaud Couloux, Stéphane Poussier, Sébastien Carrère, Emmanuelle Lauber, 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), 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-Université Paris-Saclay, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Centre IRD de Montpellier, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, University of Florida [Gainesville] (UF), Fondation Agropolis, France [AO2007 07 012], Marie Curie Outgoing International Fellowship from the European Commission, 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), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Université de Toulouse (UT), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), and University of Florida [Gainesville]
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Phylogénie ,GENE-CLUSTER ,2-COMPONENT SYSTEM ,Xanthomonas albilineans ,Genome ,VITIS-VINIFERA GRAPEVINES ,PROTEIN SECRETION SYSTEMS ,Gene cluster ,Cluster Analysis ,Phylogeny ,2. Zero hunger ,Genetics ,Xylème ,0303 health sciences ,Saccharum officinarum ,biology ,ORYZAE PV. ORYZAE ,GRAM-NEGATIVE BACTERIA ,LEAF SCALD PATHOGEN ,MULTIDRUG EFFLUX PUMPS ,INNATE IMMUNITY ,PSEUDOMONAS-AERUGINOSA ,Chromosome Mapping ,Quorum Sensing ,Saccharum ,Nucleic Acid Amplification Techniques ,Signal Transduction ,Research Article ,Biotechnology ,Séquence nucléotidique ,Xanthomonas ,lcsh:QH426-470 ,Virulence Factors ,Sequence analysis ,lcsh:Biotechnology ,Pouvoir pathogène ,Immunoblotting ,Molecular Sequence Data ,Relation hôte pathogène ,03 medical and health sciences ,Species Specificity ,Xylem ,lcsh:TP248.13-248.65 ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Adhesins, Bacterial ,Gene ,H20 - Maladies des plantes ,030304 developmental biology ,Whole genome sequencing ,Génome ,Base Sequence ,Models, Genetic ,030306 microbiology ,Inverted Repeat Sequences ,Sequence Analysis, DNA ,Nucleic acid amplification technique ,15. Life on land ,biology.organism_classification ,lcsh:Genetics ,Genes, Bacterial ,ATP-Binding Cassette Transporters ,Genome, Bacterial - Abstract
Background Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa—another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. Results Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the “artillery” of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to X. albilineans that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific to X. albilineans were identified, supposing that X. albilineans has a reduced artillery compared to other pathogenic Xanthomonas species. Particular attention has therefore been given to genomic features specific to X. albilineans making it more capable of evading sugarcane surveillance systems or resisting sugarcane defense systems. Conclusions This study confirms that X. albilineans is a highly distinctive species within the genus Xanthomonas, and opens new perpectives towards a greater understanding of the pathogenicity of this destructive sugarcane pathogen.
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