MINING OF SIMPLE SEQUENCE REPEATS IN CHLOROPLAST GENOME SEQUENCE OF COCOS NUCIFERA

Simple sequence repeats (SSRs), also known as microsatellites, are found in DNA sequences and consist of short repeating motifs of 1-6 nucleotides. These repeats are ubiquitous and play an important role in the development of molecular markers. Therefore, the present analysis was conducted to mine SSRs in chloroplast genome of Cocos nucifera. A total of 44 SSRs were identified in 154.731 kb sequence mined with an average length of 18.57 bp. Depending upon the repeat unit SSRs varied in length from 12 to 132 bp. The identified SSRs showed a density of 1SSR/3.52 kb. Mononucleotides (16, 36.36%) were found to be the most abundant repeat, followed by di and tetra nucleotide repeats with same frequency (9, 20.45%), tri and penta nucleotide repeats (4, 9.09%) and hexa nucleotide repeats (2, 4.55%). Compound SSRs were completely absent in the chloroplast genome of Cocos nucifera. Most of the perfect SSRs were confined in the non-coding region of the chloroplast genome.