Computational Mining of Microsatellites in the Chloroplast Genome of Ptilidium pulcherrimum, a Liverwort

Authors

  • Asheesh Shanker Department of Bioscience and Biotechnology, Banasthali University, Banasthali-304022, Rajasthan

DOI:

https://doi.org/10.3126/ije.v3i3.11063

Keywords:

Microsatellites, Simple Sequence Repeats, Chloroplast, Bryophytes, Liverwort

Abstract

Microsatellites also known as simple sequence repeats (SSRs) are found in DNA sequences. These repeats consist of short motifs of 1-6 bp and play important role in population genetics, phylogenetics and also in the development of molecular markers. In this study chloroplastic SSRs (cpSSRs) in the chloroplast genome of Ptilidium pulcherrimum, downloaded from the National Center for Biotechnology Information (NCBI), were detected. The chloroplast genome sequence of P. pulcherrimum was mined with the help of a Perl script named MISA. A total of 23 perfect cpSSRs were detected in 119.007 kb sequence mined showing density of 1 SSR/5.17 kb. Depending on the repeat units, the length of SSRs found to be 12 bp for mono and tri, 12 to “22 bp for di, 12 to 16 bp for tetra nucleotide repeats. Penta and hexanucleotide repeats were completely absent in chloroplast genome of P. pulcherrimum. Dinucleotide repeats were the most frequent repeat type (47.83%) followed by tri (21.74%) and tetranucleotide (21.74%) repeats. Out of 23 SSRs detected, PCR primers were successfully designed for 22 (95.65%) cpSSRs.

DOI: http://dx.doi.org/10.3126/ije.v3i3.11063

International Journal of Environment Vol.3(3) 2014: 50-58

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Published

2014-09-12

How to Cite

Shanker, A. (2014). Computational Mining of Microsatellites in the Chloroplast Genome of Ptilidium pulcherrimum, a Liverwort. International Journal of Environment, 3(3), 50–58. https://doi.org/10.3126/ije.v3i3.11063

Issue

Vol. 3 No. 3 (2014)

Section

Research Papers

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