Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life, including viruses. Members of the family Closteroviridae are the largest RNA viruses and severely affect different agricultural crops worldwide, including citrus, grapevine and vegetables. | Turkish Journal of Biology Turk J Biol (2016) 40: 589-599 © TÜBİTAK doi: Research Article In silico genome-wide identification and analysis of microsatellite repeats in the largest RNA virus family (Closteroviridae) 1 1 2 3, Biju GEORGE , Binu GEORGE , Mayur AWASTHI , Ram Nageena SINGH * 1 Blessy Software Solutions, Malviya Nagar, Jaipur, Rajasthan, India 2 Mahatma Gandhi Chitrakoot Gramodaya Vishwavidhyalaya, Madhya Pradesh, India 3 Lab No. 3, Division of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi, India Received: Accepted/Published Online: Final Version: Abstract: Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life, including viruses. Members of the family Closteroviridae are the largest RNA viruses and severely affect different agricultural crops worldwide, including citrus, grapevine, and vegetables. Here we identified and systematically analyzed the nature and distribution of both simple and complex microsatellites present in the complete genome of 36 species belonging to Closteroviridae. Our results showed, in all analyzed genomes, that neither genome size nor GC content had any influence on number, relative abundance, or relative density of microsatellites. For each genome, dinucleotide repeats were found to be highly predominant and AT/TA and AG/GA were the two most abundant dinucleotide repeat motifs. Repeats larger than trinucleotide were relatively rare in these viral genomes. Comparative study of occurrence, abundance, and density of microsatellites among available RNA and DNA viral genomes indicated that simple repeats were less abundant in genomes of Closteroviridae. To our knowledge, this is the first analysis of microsatellites occurring in the largest viral genome that infects plants. Characterization of such variations in repeat sequences would be important in deciphering the origin, .
