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Mining of simple sequence repeats in the Genome of Gentianaceae

1, 1★, 2, 3★ Corresponding author

  1. 1Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu
  2. 2Plant Cell and Molecular Biology Laboratory, Department of Biotechnology, Karunya University, Coimbatore, Tamil Nadu
  3. 3Molecular Biology and Bioinformatics Laboratory, Central Plantation Crops Research Institute, Kasaragod, Kerala, India.

CORRESPONDENCE

P. T. V. Lakshmi

Phytomatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu

Volume 3, Issue 1 · pp. 19-29 · 2011 · DOI: 10.4103/0974-8490.79111

ABSTRACT

Simple sequence repeats (SSRs) or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI). Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 –-hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16%) among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.

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    Sathishkumar, R., Lakshmi, P. T. V., Annamalai, A., & Arunachalam, V. (2011). Mining of simple sequence repeats in the Genome of Gentianaceae. Pharmacognosy Research, 3(1), 19-29. https://doi.org/10.4103/0974-8490.79111

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    © 2011 Author(s)

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as the author is credited and the new creations are licensed under the identical terms. CC BY-NC-SA 4.0