In silico analysis of genomic fingerprinting using highly repetitive sequences (HIPs, STRR and ERIC) to differentiate close cyanobacteria strains, isolated from different Climatic/Geographic Regions and Habitats

Nowadays cyanobacterial taxonomy has been considerably changed due to the study of previously uninvestigated regions as well as introduction of molecular tools. However molecular analysis without detail morphological study gives only limited information on the organism. That is several years that we could collect, isolate and purify successfully, different strains of cyanobacteria and make a cyanobacteria culture Collection (CCC) in Science and Research Branch, Islamic Azad University. Through a polyphasic approach, the differences in morphological and genotypic features of different strains were investigated. Challenges arose when the two strains collected from agricultural areas of Kermanshah identified as Calothrix, because of early unbranched filaments, narrow cells and ending by heterocysts. However, Along with the progression of growth, branching arise. Morover, two Nostoc strains islated from salt water of Golestan provice, could not be discriminated by cloned 16S rRNA and ITS genes sequencing and also descrominateling of closely relates Nostoc species isolated form dry limestones of five different province was very problematic, which generates confusing in classification. Due to entirely to an almost complete lack of information concerning which parts of the morphology if any of cyanobacteria are constant and which are not, PCR-based techniques based on fingerprinting of repetitive DNA fragments including the Highly iterated palindromes (HIP1), short tandemly repeated repetitive (STRR) and Enterobacterial Repetitive Intergenic Consensus (ERIC) has been used for assessing better resolution amongst closely related cyanobacteria strains. The presence or absence of distinct and reproducible bands in each of the individual DNA fingerprinting pattern was converted into binary data, and the pooled binary data were used to construct a composite dendrogram. The BioDiversity Pro software was used to perform the hierarchical analyses using the Jaccard cluster analysis option. The results showed 100 % polymorphism and each marker produced unique and strain-specific banding pattern. This study highlights the efficiency of this technique for assessing proximity of small number of strains, but probably for larger number of strains belonging to very closely related orders, the inclusion of DNA fingerprints in conjunction with other molecular tools would be necessary for better resolution of genetic diversity, genetic proximity, and taxonomic affiliation.

کلیدواژه ها:

fingerprinting of repetitive DNA fragments ، HIPs ، STRR ، ERIC