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Differential distribution and occurrence of simple sequence repeats in diverse geminivirus genomes

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Abstract

Microsatellites are tandem repeat sequences with repeat unit of one to six base pairs. Although, microsatellites have been studied in eukaryotes as well as prokaryotes, information on their occurrence on virus genomes is limited. We examined microsatellite distribution in 263 complete geminivirus genomes. Results indicated microsatellites to be an important component of geminiviral genomes. For each geminiviral genome, mono- and dinucleotide repeats were found to be highly predominant. Occurrence of microsatellites within geminiviral genome is significantly lesser than organisms with higher genome sizes and their number decreased with an increase in the length of repeat unit. Repeats of AT/TA, GT/TG, CT/TC, CTT/TTC, and GAA/AAG occurred with high frequency, whereas CG/GC, CGA/AGC, AAC/CAA, and GCT/TCG repeats had rare incidence. Interesting observation related to differential distribution of simple sequence repeats in genomic components of begomoviruses has been noted. We discussed the possible reasons for the observed divergence. To our knowledge, this is the first analysis of microsatellites occurring in any ssDNA viral genome for such purposes and represents a general approach for analysis of other viral genomes. The presence of microsatellites in geminiviral genomes may be used to obtain information regarding viral genetic diversity, evolution, and strain (isolate) identification.

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Acknowledgments

Financial support from the UGC Capacity Build Up and UGC Resource Net working provided by JNU to SC is gratefully acknowledged.

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Authors and Affiliations

  1. Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    B. George, Ch. Mashhood Alam & S. Chakraborty

  2. Department of Biotechnology, Jamia Hamdard University, New Delhi, India

    B. George & S. K. Jain

  3. Department of Botany, Patna University, Patna, Bihar, India

    Ch. Mashhood Alam & Ch. Sharfuddin

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  1. B. George
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  2. Ch. Mashhood Alam
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  3. S. K. Jain
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  5. S. Chakraborty
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Correspondence to S. Chakraborty.

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George, B., Mashhood Alam, C., Jain, S.K. et al. Differential distribution and occurrence of simple sequence repeats in diverse geminivirus genomes. Virus Genes 45, 556–566 (2012). https://doi.org/10.1007/s11262-012-0802-1

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  • DOI: https://doi.org/10.1007/s11262-012-0802-1

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