16S–23S rRNA Intergenic Spacer Region Variability in the Genus Frankia

• DOI: 10.1007/s00248-010-9641-6
• Publication Date: 2010-02-23T15:22:44Z
• Authors: Faten Ghodhbane-G...; Imen Nouioui; Mohamed Chair; Abdellatif Boudabous; Maher Gtari
• Keywords: DNA, Bacterial; 0301 basic medicine; Polymorphism, Genetic; Base Sequence; Molecular Sequence Data; Sequence Analysis, DNA; Polymerase Chain Reaction; RNA, Ribosomal, 23S; 03 medical and health sciences; RNA, Ribosomal, 16S; Frankia; DNA, Intergenic; Sequence Alignment; Phylogeny

16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.