Shanker, A. Simple sequence repeats mining using computational approach in chloroplast genome of Marchantia polymorpha
Arctoa (2014) 23: 145-149
Simple sequence repeats (SSRs) or microsatellites are found in DNA sequences and consist of short repeat motifs of 1-6 bp. These repeats play important role in the development of molecular markers, phylogenetics, population genetics and evolutionary biology. The present analysis was conducted to detect chloroplastic SSRs (cpSSRs) in Marchantia polymorpha. The chloroplast genome sequence of M. polymorpha was downloaded from the National Center for Biotechnology Information (NCBI) and mined with the help of a Perl script named MISA. A total of 66 cpSSRs were detected in 121.024 kb sequence mined showing density of 1 SSR/1.83 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 17 bp for mono, 12 to 64 bp for di, 12 to 21 bp for tri, 12 to 24 bp for tetra, 15 bp for penta and 18 bp for hexa nucleotide repeats. Mononucleotide repeats were the most frequent repeat type (42.42%) followed by dinucleotide (25.76%) and tetranucleotide (21.21%) repeats. PCR primers were successfully designed for 45 (68.18%) cpSSRs of M. polymorpha.