Genomic fingerprinting of Frankia strains by PCR-based techniques. Assessment of a primer based on the sequence of 16S rRNA gene of Escherichia coli

• Published in: Plant and soil 2003-07, Vol.254 (1), p.115-123
• Main Authors: Igual, José M., Valverde, Angel, Rivas, Raúl, Mateos, Pedro F., Rodríguez-Barrueco, C., Martínez-Molina, Eustoquio, Cervantes, Emilio, Velázquez, Encarna
• Format: Article
• Language: English
• Subjects: Actinomycetes; Bacteria; Bacteriology; Biological and medical sciences; Biological taxonomies; Deoxyribonucleic acid; DNA; E coli; Frankia; Fundamental and applied biological sciences. Psychology; Genetics; Genomics; Host plants; Microbiology; Nodules; Plants; Polymerase chain reaction; Ribosomal DNA; Root nodules; Symbiosis; Systematics
• ISSN: 0032-079X; 1573-5036
• DOI: 10.1023/A:1024978426934

Polimerase Chain Reaction (PCR)-based genomic fingerprints of 16 Frankia isolates were obtained using two different primers. rep-PCR DNA fingerprints were obtained by using DR1R primer, and Randomly Amplified Polymorphic DNA (RAPD) fingerprints by using a large primer derived from the 16S rDNA sequence of Escherichia coli (879F primer). According to the results obtained, primer DR1R generates strain-specific patterns. However, primer 879F yielded an identical band patterns in two Frankia strains, CcI3 and UGL 020603, isolated from different Casuarina species and geographical origins, indicating that it could identify genomic fingerprints at a higher taxonomic level (subspecies or species) than DR1R primer. To verify this hypothesis, we tested the primer 879F with eight strains of Clavibacter michiganensis, another actinobacterium with high G+C content, which includes several well-defined subspecies. Primer 879F identified a unique band pattern in all strains within the same subspecies but different patterns for other subspecies, indicating that it generates subspecies-specific genomic fingerprints. Consequently, Frankia Cc13 and Frankia UGL 020603 should be included in the same subspecies and the remaining Frankia strains used in this study in different subspecies. An UPGMA dendrogram of the 879F-PCR fingerprint patterns shows that the Frankia strains used in this study could be clustered into groups that broadly reflects the host plants from which they were derived. These results are consistent with those obtained by other authors using different techniques. Because primer 879F yields genomic fingerprints at taxonomic level upper than strain level, it may be a valuable tool in the polyphasic approach to Frankia taxonomy, where other classical taxonomic methods are barely applicable. Taking into account that several primers can be designed from ribosomal sequences in order to obtain RAPD patterns, we propose to name these methods according to the position of such primers in the 16S rRNA sequences of Escherichia coli. In this way, we name 879F-RAPD fingerprinting the procedure used in this study.