Genomic Fingerprinting Using Highly Repetitive Sequences to Differentiate Close Cyanobacterial Strains

Background: Cyanobacterial taxonomy has experimented considerable changes due to the exploration of previously uninvestigated regions as well as the introduction of molecular tools. Challenges arose when strains collected from agricultural areas, salt waters and dry limestone did not reveal remarkable morphological differences and had a high level of similarity in the phylogeny of 16S rDNA gene sequences. The aim of the present investigation was to fingerprint members of the genera Calothrix and Nostoc based on the repetitive DNA sequences, as molecular markers for the detection of phylogenetic affinities and molecular diversity. Methods: In this research, through a polyphasic approach, the differences in morphological and genotypic features of different strains were investigated. Bacteria free cyanobacterial clones were prepared followed by morphological characterization, genomic DNA extraction and PCR with 16S rRNA, ERIC, STRR1a and HIP primers. Then the phylogenetic analyses of partial 16S rRNA genes and fingerprints were performed. Results: The results showed each marker producing unique and strain-specific banding pattern, thus highlighting the efficiency of this technique in the assessment of proximity between closely related cyanobacterial strains isolated from different climatic/geographic regions and habitats. Conclusions: This case is the first documented genomic fingerprinting from seven close cyanobacterial strains in Iran.