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

Authors

  • Asheesh Shanker Centre for Biological Sciences School of Earth, Biological and Environmental Sciences Central University of South Bihar BIT Campus, Patna-800014, Bihar, India.

DOI:

https://doi.org/10.14719/pst.2016.3.2.206

Keywords:

Bryophytes, chloroplast genome, microsatellites, moss, Tetraphis

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.

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Author Biography

Asheesh Shanker, Centre for Biological Sciences School of Earth, Biological and Environmental Sciences Central University of South Bihar BIT Campus, Patna-800014, Bihar, India.

Associate ProfessorCentre for Biological SciencesSchool of Earth, Biological and Environmental SciencesCentral University of South BiharBIT Campus, Patna-800014, Bihar, India.

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Published

13-06-2016

How to Cite

1.
Shanker A. Detection of simple sequence repeats in the chloroplast genome of Tetraphis pellucida Hedw. Plant Sci. Today [Internet]. 2016 Jun. 13 [cited 2024 Nov. 4];3(2):207-10. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/206

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Section

Special Section: New Frontiers in Cryptogamic Botany

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