ISSN 0026-2617, Microbiology, 2013, Vol. 82, No. 6, pp. 801–808. © Pleiades Publishing, Ltd., 2013. 801 1 Cyanobacteria are a morphologically diverse group of organisms ranging from unicellular to filamentous forms. These oxygenic, photoautotrophic prokaryotes are among the most ancient organisms inhabiting the Earth’s environment [1, 2]. Cyanobacteria exhibit remarkable diversity in their morphological, develop- mental and physiological behavior [3]. Nevertheless, in the course of evolution, cyanobacteria have devel- oped some unique physiological and morphological features to respond to the changes in environmental parameters such as light, temperature, pH and nutri- ents [4]. As a result of these adaptations, they are present in nearly all the ecosystems [1, 5]. The taxonomic status of the cyanobacteria was determined based extensively on their morphological and physiological features. It was observed, however, that the morphology and physiology of environmental isolates was altered in laboratory conditions [6]. In the recent times the development of both bioinformatics and molecular techniques made it possible to mine the genome of the microorganisms for identifying unique sequences that can be used to identify the microorgan- isms both among and within a group [7–11]. Although 16S rRNA gene has been extensively used in taxo- nomic and phylogenetic studies involving all the ba 1 The article is published in the original. 2 Corresponding author; e-mail: akmishraau@rediffmail.com; akmishraau@hotmail.com 3 Present address: Department of Botany, Guru Ghasidas Vishwavidyalaya, Bilaspur, Chhattisgarh. terial phyla as a standard marker, due to its conserva- tive nature it does not always provide adequate dis- criminatory power for identification of cyanobacteria, even when the species are physiologically distinct [12, 13]. Similarly, a number of authors demonstrated the usefulness of other markers; the 16S–23S internal transcribed spacer, phycocyanin-encoding PC–IGS region [14], the house keeping gene (rpoC1) [15], and the nifH [11, 16] and nifD genes [17] have been widely used to detect genetic relatedness and molecular phy- logeny within the cyanobacterial lineage. While repetitive sequences have been increasingly identified in prokaryotic genomes but their function, maintenance and occurrence still remain obscure. The widespread distribution and sufficient conservation of these repetitive sequences within the genome have been used as a supplant technique for the identifica- tion of species or strains, as well as in diversity analysis [18, 19]. Ever since their discovery, short tandemly repeated repetitive sequences (STRR sequences) have been widely used to differentiate between environ- mental cyanobacterial isolates. These heptanuclotide repeat sequences have been identified in several cyanobacterial genera and species, mostly in the case of heterocystous cyanobacteria, viz. Calothrix sp. and also some non-heterocystous cyanobacteria [20, 21]. Highly Iterated Palindrome sequence commonly referred to as HIP1 is a repetitive eight- base sequence (5'-GCGATCGC-3'), well represented in the cyano- bacterial genome and is hypothesized to be a recombi- nation hotspot [19, 22, 23]. HIP1 sequencing has also Fingerprinting and Phylogeny of Some Heterocystous Cyanobacteria Using Short Tandemly Repeated Repetitive and Highly Iterated Palindrome Sequences 1 E. Shukla, S. S. Singh 3 , and A. K. Mishr 2 Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005 India Received December 15, 2012 Abstract—The presence of repeated DNA, viz. short tandemly repeated repetitive (STRR) and highly iter- ated palindrome (HIP) sequences was used as a typing technique for assessing genetic variability and phylo- genetic relatedness of heterocystous cyanobacteria. Primers analogous to the STRR and HIP sequences were used to generate specific fingerprints for the twelve heterocystous cyanobacterial strains and a dendrogram was constructed. STRRmod and HIPTG primers revealed 100% polymorphism and yielded almost identical patterns. Anabaena sp. PCC 7120 clustered with Nostoc muscorum with both primers. Primer STRRmod sup- ported the heterogeneity between Nostoc and Anabaena but HIPTG placed these two genera distinctly apart. STRRmod and HIPTG revealed that the members of the two orders were intermixed and thus suggesting a monophyletic origin of heterocystous cyanobacteria. Keywords: repetitive DNA sequences, heterocystous cyanobacteria, typing, STRRmod, HIP DOI: 10.1134/S0026261714010123 EXPERIMENTAL ARTICLES