title: Sequence analysis of rpoB and rpoD gene fragments reveals the phylogenetic diversity of actinobacteria of genus Frankia.
abstract: Partial rpoD, rpoB, and 16S rRNA gene sequences were obtained from databases and (or) amplified from 12 strains of Frankia. These strains belonged to either Cluster 1 (Alnus-, Myrica-, Comptonia-, and Casuarina-infective strains) or Cluster 3 (Elaeagnus-infective strain). An rpoD gene-based PCR approach was designed to allow the detection of frankiae in complex samples. Additionally, partial gene sequences obtained using 2 rpoB gene primer sets (named rpoB-1 and rpoB-2) were used to generate phylogenetic eurograms to find a molecular tool able to assess biodiversity among Frankia strains. The rpoB-2 primer set allowed separation of closely related strains and groupings representative of host plant compatibility groups. One exception to this was for strains ACN10a and ACN14a, isolated from the same geographical location. Results obtained showed that rpoB-2 is a tool of great interest to evaluate relatedness of Frankia strains, and assess biodiversity in this genus. Additionally, since rpoB-2 phylogenetic profiles of the Frankia strains studied reflected the species of host plants they were isolated from, the study of rpoB (a house-keeping gene) shows promise for future ecological studies on these symbioses.
authors.affiliation: Centre d'étude et de valorisation de la diversité microbienne, Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.
authors.forename: Audrey
authors.initials: A
authors.lastname: Bernèche-D'Amours
authors.forename: Mariana Gabriela
authors.initials: MG
authors.lastname: Ghinet
authors.forename: Julie
authors.initials: J
authors.lastname: Beaudin
authors.forename: Ryszard
authors.initials: R
authors.lastname: Brzezinski
authors.forename: Sébastien
authors.initials: S
authors.lastname: Roy
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D040161:Frankia / Q000145:classification / Q000235:genetics*; D005798:Genes, Bacterial; D014644:Genetic Variation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012808:Sigma Factor / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases