title: PCR primers based on different portions of insertion elements can assist genetic relatedness studies, strain fingerprinting and species identification in rhizobia.
abstract: Using the sequence of an insertion element originally found in Rhizobium sullae, the nitrogen-fixing bacterial symbiont of the legume Hedysarum coronarium, we devised three primer pairs (inbound, outbound and internal primers) for the following applications: (a) tracing genetic relatedness within rhizobia using a method independent of ribosomal inheritance, based on the presence and conservation of IS elements; (b) achieve sensitive and reproducible bacterial fingerprinting; (c) enable a fast and unambiguous detection of rhizobia at the species level. In terms of taxonomy, while in line with part of the 16S rRNA gene- and glutamine synthetase I-based clustering, the tools appeared nonetheless more coherent with the actual geographical ranges of origin of rhizobial species, strengthening the European-Mediterranean connections and discerning them from the asian and american taxa. The fingerprinting performance of the outward-pointing primers, designed upon the inverted repeats, was shown to be at least as sensitive as BOX PCR, and to be functional on a universal basis with all 13 bacterial species tested. The primers designed on the internal part of the transposase gene instead proved highly species-specific for R. sullae, enabling selective distinction from its most related species, and testing positive on every R. sullae strain examined, fulfilling the need of PCR-mediated species identification. A general use of other IS elements for a combined approach to rhizobial taxonomy and ecology is proposed.
authors.affiliation: C.N.R., Istituto per il Sistema Produzione, Animale in Ambiente Mediterraneo ISPAAM, Sezione di Sassari, c\o Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari, Via Enrico de Nicola 07100, Sassari, Italy.
authors.forename: Rosella
authors.initials: R
authors.lastname: Muresu
authors.forename: Leonardo
authors.initials: L
authors.lastname: Sulas
authors.forename: Elisa
authors.initials: E
authors.lastname: Polone
authors.forename: Andrea
authors.initials: A
authors.lastname: Squartini
mesh_terms: D001483:Base Sequence; D002965:Classification / Q000379:methods; D016000:Cluster Analysis; D019295:Computational Biology; D016172:DNA Fingerprinting / Q000379:methods; D017931:DNA Primers / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D007091:Image Processing, Computer-Assisted; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012231:Rhizobium / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D004251:DNA Transposable Elements