title: New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination.
abstract: Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants.
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France marie-agnes.jacques@angers.inra.fr.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Jacques
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France Anses Laboratoire de la Santé des Végétaux, Angers, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Denancé
authors.affiliation: Anses Laboratoire de la Santé des Végétaux, Angers, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Legendre
authors.affiliation: Nestlé R&D Tours, Tours, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Morel
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France.
authors.forename: Martial
authors.initials: M
authors.lastname: Briand
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France Anses Laboratoire de la Santé des Végétaux, Angers, France Nestlé R&D Tours, Tours, France.
authors.forename: Stelly
authors.initials: S
authors.lastname: Mississipi
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Durand
authors.affiliation: Anses Laboratoire de la Santé des Végétaux, Angers, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Olivier
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France.
authors.forename: Perrine
authors.initials: P
authors.lastname: Portier
authors.affiliation: Anses Laboratoire de la Santé des Végétaux, Angers, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Poliakoff
authors.affiliation: Nestlé R&D Tours, Tours, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Crouzillat
mesh_terms: D003069:Coffee / Q000382:microbiology*; D004484:Ecuador; D005602:France; D014644:Genetic Variation; D016680:Genome, Bacterial; D059765:Homologous Recombination; D008800:Mexico; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012703:Serotyping; D044167:Xylella / Q000145:classification / Q000235:genetics* / Q000254:growth & development* / Q000276:immunology
chemical_list: D003069:Coffee