title: Classification of Isolates from thePseudomonas fluorescensComplex into Phylogenomic Groups Based in Group-Specific Markers.
abstract: ThePseudomonas fluorescenscomplex of species includes plant-associated bacteria with potential biotechnological applications in agriculture and environmental protection. Many of these bacteria can promote plant growth by different means, including modification of plant hormonal balance and biocontrol. TheP. fluorescensgroup is currently divided into eight major subgroups in which these properties and many other ecophysiological traits are phylogenetically distributed. Therefore, a rapid phylogroup assignment for a particular isolate could be useful to simplify the screening of putative inoculants. By using comparative genomics on 71P. fluorescensgenomes, we have identified nine markers which allow classification of any isolate into these eight subgroups, by a presence/absence PCR test. Nine primer pairs were developed for the amplification of these markers. The specificity and sensitivity of these primer pairs were assessed on 28 field isolates, environmental samples from soil and rhizosphere and tested byin silicoPCR on 421 genomes. Phylogenomic analysis validated the results: the PCR-based system for classification ofP. fluorescensisolates has a 98.34% of accuracy and it could be used as a rapid and simple assay to evaluate the potential of anyP. fluorescenscomplex strain.
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Garrido-Sanz
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Arrebola
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Martínez-Granero
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Sonia
authors.initials: S
authors.lastname: García-Méndez
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Candela
authors.initials: C
authors.lastname: Muriel
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Esther
authors.initials: E
authors.lastname: Blanco-Romero
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Martín
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Rivilla
authors.affiliation: Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Redondo-Nieto
keywords: PCR; Pseudomonas fluroescens complex; classification; phylogroups