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

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Abstract

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.

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Acknowledgments

This work was supported by grants from the High Education and Scientific Research Ministry of Tunisia and the EU Project BIODESERT 245756 (FP7-Capacities-RegPot 2009-2). The authors were grateful to Professor D. P. Labeda (NRRL bacterial collection) for supplying Frankia strains and to Professor John D. Tjepkema (University of Maine, USA) for providing Ceanothus nodules.

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  1. Laboratoire Microorganismes and Biomolécules Actives, Département de Biologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092, Tunis, Tunisia

    Faten Ghodhbane-Gtari, Imen Nouioui, Mohamed Chair, Abdellatif Boudabous & Maher Gtari

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  1. Faten Ghodhbane-Gtari
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  2. Imen Nouioui
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  3. Mohamed Chair
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  4. Abdellatif Boudabous
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  5. Maher Gtari
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Correspondence to Maher Gtari.

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Ghodhbane-Gtari, F., Nouioui, I., Chair, M. et al. 16S–23S rRNA Intergenic Spacer Region Variability in the Genus Frankia . Microb Ecol 60, 487–495 (2010). https://doi.org/10.1007/s00248-010-9641-6

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  • DOI: https://doi.org/10.1007/s00248-010-9641-6

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