title: Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers.
abstract: Biovar 1 of the genus Agrobacterium consists of at least nine genomic species that have not yet received accepted species names. However, rapid identification of these organisms in various biotopes is needed to elucidate crown gall epidemiology, as well as Agrobacterium ecology. For this purpose, the AFLP methodology provides rapid and unambiguous determination of the genomic species status of agrobacteria, as confirmed by additional DNA-DNA hybridizations. The AFLP method has been proven to be reliable and to eliminate the need for DNA-DNA hybridization. In addition, AFLP fragments common to all members of the three major genomic species of agrobacteria, genomic species G1 (reference strain, strain TT111), G4 (reference strain, strain B6, the type strain of Agrobacterium tumefaciens), and G8 (reference strain, strain C58), have been identified, and these fragments facilitate analysis and show the applicability of the method. The maximal infraspecies current genome mispairing (CGM) value found for the biovar 1 taxon is 10.8%, while the smallest CGM value found for pairs of genomic species is 15.2%. This emphasizes the gap in the distribution of genome divergence values upon which the genomic species definition is based. The three main genomic species of agrobacteria in biovar 1 displayed high infraspecies current genome mispairing values (9 to 9.7%). The common fragments of a genomic species are thus likely "species-specific" markers tagging the core genomes of the species.
authors.affiliation: Ecologie Microbienne, Université Claude Bernard-Lyon 1, Domaine scientifique de La Doua, 16 rue Raphaël Dubois, 69622 Villeurbanne cedex, France.
authors.forename: Perrine
authors.initials: P
authors.lastname: Portier
authors.forename: Marion
authors.initials: M
authors.lastname: Fischer-Le Saux
authors.forename: Christophe
authors.initials: C
authors.lastname: Mougel
authors.forename: Catherine
authors.initials: C
authors.lastname: Lerondelle
authors.forename: David
authors.initials: D
authors.lastname: Chapulliot
authors.forename: Jean
authors.initials: J
authors.lastname: Thioulouse
authors.forename: Xavier
authors.initials: X
authors.lastname: Nesme
mesh_terms: D015373:Bacterial Typing Techniques; D004783:Environmental Microbiology; D005819:Genetic Markers; D016680:Genome, Bacterial; D006801:Humans; D009693:Nucleic Acid Hybridization; D012150:Polymorphism, Restriction Fragment Length; D012231:Rhizobium / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D013045:Species Specificity
chemical_list: D005819:Genetic Markers