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Genome wide survey and analysis of microsatellites in Tombusviridae family

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Abstract

Microsatellites are small repetitive sequences found in all kingdoms of life including viruses. Members of the Tombusviridae family severely affect growth of wide range of plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 47 species of Tombusviridae family. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, dinucleotide repeats followed by mononucleotide repeats were found to be highly predominant. Mononucleotide repeats were found to be underrepresented in majority of Tombusviridae genomes. Poly G and Poly C repeats were more abundant as compared to poly A or poly T nucleotides. TG/GT and AG/CA was the most abundant dinucleotide repeat motif observed in Tombusviridae genomes. Repeats larger than trinucleotide were never found in these viral genomes. Comparative study of relative abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were lower than many RNA virus genomes. To our knowledge, this is the first analysis of microsatellites occurring in Tombusviridae genomes. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.

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Acknowledgments

We acknowledge Blessy software solution for support.

Conflict of interest

Authors declare that they do not have any conflict of interest regarding this research work.

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Authors and Affiliations

  1. Blessy Software Solutions, Sector 4/441, Malviya Nagar, Jaipur, 302017, Rajasthan, India

    Biju George & Binu George

  2. Mahatma Gandhi Chitrakoot Gramodaya Vishwavidhyalaya, Chitrakoot, 485334, Madhya Pradesh, India

    Mayur awasthi

  3. Division of Microbiology, Indian Agricultural Research Institute, Pusa, 110012, New Delhi, India

    Ram Nageena Singh

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  1. Biju George
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  2. Binu George
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  3. Mayur awasthi
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  4. Ram Nageena Singh
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Correspondence to Biju George or Ram Nageena Singh.

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George, B., George, B., awasthi, M. et al. Genome wide survey and analysis of microsatellites in Tombusviridae family. Genes Genom 37, 657–667 (2015). https://doi.org/10.1007/s13258-015-0295-0

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  • DOI: https://doi.org/10.1007/s13258-015-0295-0

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