Common, Unique and Polymorphic Simple Sequence Repeats in Chloroplast Genomes of genus Arabidopsis

Kumar Sonu, Shanker Asheesh*

Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Pub Email:
Doi: 10.5958/2229-4473.2018.00043.5
First Page: 125
Last Page: 131
Views: 1212

Keywords: Simple sequence repeats, Chloroplast, <I>A rabidopsis</I>, Primer, Transferability.


Simple sequence repeats (SSRs) consists of 1–6 nucleotides and are widely used molecular marker. These repeats are found in almost all organisms. However, the distribution of chloroplast SSRs (cpSSRs) is not well understood in genus A rabidopsis. To annotate the current knowledge of putative polymorphic, common, and unique cpSSRs of genus Arabidopsis, a sum of 628 cpSSRs were mined. Mononucleotides (338, 53.82%) were most abundant followed by tetranucleotides (133, 21.18%), di-nucleotides (79, 12.58%), tri-nucleotides (41, 6.53%), penta-nucleotides (19, 3.03%), and hexa-nucleotide (8, 1.27%) repeats. Apart from this, 10 compound (1.60%) cpSSRs were detected. Common, unique, and polymorphic cpSSRs were also identified. Primer pairs were designed to study cross species transferability. The cpSSRs identified in this study can be helpful in species identification, genetic mapping, and diversity studies of genus Arabidopsis.

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Author Information

Kumar Sonu Shanker Asheesh*
Bioinformatics Programme, Centre for Biological Sciences, Central University of South Bihar, Patna campus-800014, India

*Corresponding author: Bioinformatics Programme, Centr e for Biological Sciences, Central University of South Bihar, Patna campus-800014, India. E-mail: