1. Genomospecies identification and phylogenomic relevance of AFLP analysis of isolated and non-isolated strains of Frankia spp
- Author
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Xavier Nesme, M. Valdés, Maria P. Fernandez, G.H.H. Bautista, H.A. Cruz, H.A. Mendoza, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Instituto Politecnico Nacional [Mexico] (IPN), CONACYT (48044), Mexico-France, and French Region Rhone-Alpes
- Subjects
DNA, Bacterial ,AFLP ,[SDV]Life Sciences [q-bio] ,Frankia ,Biology ,Subspecies ,EVOLUTIONARY GENOMIC DISTANCE ,Applied Microbiology and Biotechnology ,Microbiology ,Genome ,Polymerase Chain Reaction ,03 medical and health sciences ,Magnoliopsida ,Species Specificity ,Phylogenetics ,FRANKIA PHYLOGENY ,Botany ,Amplified Fragment Length Polymorphism Analysis ,ADN BACTERIEN ,Symbiosis ,Genome size ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Genetics ,Frankia alni ,0303 health sciences ,DISTANCE GENETIQUE ,Phylogenetic tree ,030306 microbiology ,GENOMOSPECIES ,Genetic Variation ,biology.organism_classification ,UNCULTURED STRAINS ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,POLYMORPHISME DE LONGUEUR DE FRAGMENTS AMPLIFIES ,Amplified fragment length polymorphism ,HYBRIDATION DNA ,Root Nodules, Plant ,Genome, Bacterial - Abstract
Amplified fragment length polymorphism (AFLP) was tested as an alternative to the DNA-DNA hybridization technique (DDH) to delineate genomospecies and the phylogenetic structure within the genus Frankia. Forty Frankia strains, including representatives of seven DDH genomospecies, were typed in order to infer current genome mispairing (CGM) and evolutionary genomic distance (EGD). The constructed phylogeny revealed the presence of three main clusters corresponding to the previously identified host-infecting groups. In all instances, strains previously assigned to the same genomospecies were grouped in coherent clusters. A highly significant correlation was found between DDH values and CGM computed from AFLP data. The species definition threshold was found to range from 0.071 to 0.098 mismatches per site, according to host-infecting groups, presumably as a result of large genome size differences. Genomic distances allowed new Frankia strains to be assigned to nine genomospecies previously determined by DDH. The applicability of AFLP for the characterization of uncultured endophytic strains was tested on experimentally inoculated plants and then applied to Alnus incana and A. viridis field nodules hosting culture refractory spore-positive (Sp+, that sporulate in planta) strains. Only 1.3% of all AFLP fragments were shown to be generated by the contaminant plant DNA and did not interfere with accurate genomospecies identification of strains. When applied to field nodules, the procedure revealed that Alnus Sp+ strains were bona fide members of the Alnus-Myrica host infecting group. They displayed significant genomic divergence from genomospecies G1 of Alnus infecting strains (i.e. Frankia alni) and thus may belong to another subspecies or genomospecies. (C) 2011 Elsevier GmbH. All rights reserved.
- Published
- 2011