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Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes

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Abstract

Microsatellites also known as Simple Sequence Repeats are short tandem repeats of 1–6 nucleotides. These repeats are found in coding as well as non-coding regions of both prokaryotic and eukaryotic genomes and play a significant role in the study of gene regulation, genetic mapping, DNA fingerprinting and evolutionary studies. The availability of 73 complete genome sequences of cyanobacteria enabled us to mine and statistically analyze microsatellites in these genomes. The cyanobacterial microsatellites identified through bioinformatics analysis were stored in a user-friendly database named CyanoSat, which is an efficient data representation and query system designed using ASP.net. The information in CyanoSat comprises of perfect, imperfect and compound microsatellites found in coding, non-coding and coding-non-coding regions. Moreover, it contains PCR primers with 200 nucleotides long flanking region. The mined cyanobacterial microsatellites can be freely accessed at www.compubio.in/CyanoSat/home.aspx. In addition to this 82 polymorphic, 13,866 unique and 2390 common microsatellites were also detected. These microsatellites will be useful in strain identification and genetic diversity studies of cyanobacteria.

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Acknowledgments

AS is thankful to University Grants Commission, India for providing financial support (Major Research Project F.No. 42-138/2013).

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Authors and Affiliations

  1. Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan, 304022, India

    Ritika Kabra, Aditi Kapil, Kherunnisa Attarwala & Asheesh Shanker

  2. Department of Mathematics and Statistics, Banasthali University, Banasthali, Rajasthan, 304022, India

    Piyush Kant Rai

  3. Bioinformatics Programme, Centre for Biological Sciences, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, BIT Campus, Patna, Bihar, 800014, India

    Asheesh Shanker

Authors
  1. Ritika Kabra
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  2. Aditi Kapil
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  3. Kherunnisa Attarwala
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  4. Piyush Kant Rai
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  5. Asheesh Shanker
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Correspondence to Asheesh Shanker.

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Ritika Kabra and Aditi Kapil are joint first authors.

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Kabra, R., Kapil, A., Attarwala, K. et al. Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes. World J Microbiol Biotechnol 32, 71 (2016). https://doi.org/10.1007/s11274-016-2061-0

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  • DOI: https://doi.org/10.1007/s11274-016-2061-0

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