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

Detection of simple sequence repeats in the chloroplast genome of Tetraphis pellucida Hedw.

“…The density of cpSSRs in T. pellucida (1 SSR/3.04 kb) found to be lower than the density of cpSSRs in Anthoceros formosae (1 SSR/2.4 kb; Shanker, 2013d) and Marchantia polymorpha (1 SSR/1.83 kb; Shanker, 2014c), however, higher than the density of cpSSRs in Aneura mirabilis (1 SSR/5.68 kb; Shanker 2013e), Pellia endiviifolia (1 SSR/7.09 kb; Shanker, 2014b), and Ptilidium pulcherrimum (1 SSR/5.17 kb; Shanker, 2014a). Moreover, it is higher than the density of EST-SSRs in barley, maize, wheat, rye, sorghum and rice (1 SSR/6.0 kb; Varshney et al 2002), cpSSRs of rice (1SSR/6.5 kb; Rajendrakumar et al, 2007), Unigene sequences of Citrus (1 SSR/12.9 kb; Shanker et al, 2007a), average density of chloroplast genomes of Rosales (1 SSR/5.12 kb; Srivastava and Shanker, 2015a) and Magnoliids (1 SSR/6.91 kb; Srivastava and Shanker, 2015b).…”

“…These repeats act as molecular markers in many plant genomes and also identified in bryophytes (Shanker, 2014a;2014b;2014c;Pandey et al, 2016). However, the distribution of SSRs in chloroplast genome of Tetraphis pellucida Hedw.…”

Potential of Microsatellites Markers for the Genetic Analysis of Bryophytes

“…1. The frequency of each SSR repeats (mono-to hexa) in four bryophytes species (Shanker 2013a(Shanker , 2013b(Shanker , 2014a(Shanker , 2014b reviewed extensively (Zane et al, 2002;Weising et al, 2005;Kalia et al, 2011). Hutsemékers et al (2008 identified 8 nuclear microsatellite loci in the aquatic moss Platyhypnidium riparioides using the microsatellite-enriched library's method.…”

“…Homoplasy is usually common in compound or interrupted repeats (Adams et al, 2004) and it can be categorized in two groups (a) Table 3. Total number of microsatellites identified by screening chloroplast genome sequence of bryophytes (Shanker et al, 2013a(Shanker et al, , 2013b(Shanker et al, , 2014a(Shanker et al, , 2014b detectable homoplasy, (b) non detectable homoplasy. The detectable homoplasy can be revealed by nucleotide sequencing.…”

A review of IJE papers: (Vol. 3, Iss. 3 & 4)

“…Several important suggestions were made to decrease the overall consumption such as: replacing the old obsolete electric wire; integrating the regulators with the ceiling fans to adjust the load based on the ambient conditions; replacing manual switches with automated sensory switches; installing occupancy sensors etc. Shanker (2014) studied the chloroplastic simple sequence repeats (cpSSRs) found in DNA sequences. Author found cpSSRs in the chloroplast genome of Ptilidium pulcherrimum, downloaded from the National Center for Biotechnology Information (NCBI).…”