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

Abstract

Simple sequence repeats (SSRs) consist of short repeat motifs of 1-6 nucleotides and are found in DNA sequences.The present study was conducted to detect SSRs in chloroplast genome of Tetraphis pellucida (Accession number: NC_024291), downloaded from the National Center for Biotechnology Information (NCBI). The sequence was mined with the help of MISA, a Perl script, to detect SSRs. The length of SSRs defined as ≥12 for mono, di, tri and tetranucleotide, ≥15 for pentanucleotide and ≥18 for hexanucleotide repeats. In total, 41 perfect microsatellites were identified in 127.489 kb sequence mined. An average length of 13.56 bp was calculated for mined SSRs with a density of 1 SSR/3.04 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 20 nt. Dinucleotides (14, 34.15%) were the most frequent repeat type, followed by tetranucleotides (10, 24.39%), trinucleotides (7, 17.07%), mononucleotides (6, 14.63%) and pentanucleotide (4, 9.76%) repeats. Hexanucleotide repeats were completely absent in chloroplast genome of Tetraphis pellucida. The mined SSRs can be used to develop molecular markers and genetic diversity studies in Tetraphis species. Keywords

In Silico Comparative Analysis of Simple Sequence Repeats in Chloroplast Genomes of Genus Nymphaea

“…Previously, using computational approaches SSRs were mined in large amount of sequence data retrieved from National Centre for Biotechnology Information (NCBI) and online databases were developed for obtained information (Kapil et al, 2014;Kumar et al, 2014;Kabra et al, 2016). The availability of nucleotide/genome sequence of various organisms in biological databases proved to be a fast and inexpensive way for computational mining of SSRs (Shanker, 2013(Shanker, , 2014Shanker, 2016;Kumar & Shanker, 2018c).…”