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.

Downloads

Download data is not yet available.

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.

References

Bell N. E., J. L. Boore, B. D. Mishler, and Hyvonen J. 2014. Organellar genomes of the four-toothed moss, Tetraphis pellucida. BMC Genomics 15: 383. doi: 10.1186/1471-2164-15-383

Kapil A., P. K. Rai and A. Shanker. 2014. ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants. Database (Oxford) 2014 doi: 10.1093/database/bau107.

Kumar M., A. Kapil and A. Shanker. 2014. MitoSatPlant: mitochondrial microsatellites database of viridi plantae. Mitochondrion 19: 334-337. doi: 10.1016/j.mito.2014.02.002

Rajendrakumar P., A. K. Biswal, S. M. Balachandran Srinivasarao K, and R. M. Sundaram. 2007. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics 23: 1-4.

Pandey S., V. Sharma and A. Alam. 2016. Potential of microsatellites markers for the genetic analysis of bryophytes. Not Sci Biol 8(1): 37-46. doi: 10.15835/nsb.8.1.9748

Shanker A. 2012. Chloroplast genomes of bryophytes: A review. Arch Bryol 143: 1-5.

Shanker A. 2013a. Paraphyly of bryophytes inferred using chloroplast sequences. Arch Bryol 163: 1-5.

Shanker A. 2013b. Inference of bryophytes paraphyly using mitochondrial genomes. Arch Bryol 165: 1-5.

Shanker A. 2013c. Combined data from chloroplast and mitochondrial genome sequences showed paraphyly of bryophytes. Arch Bryol 171: 1-9.

Shanker A. 2013d. Identification of microsatellites in chloroplast genome of Anthoceros formosae. Arch Bryol 191: 1-6.

Shanker A. 2013e. Mining of simple sequence repeats in chloroplast genome of a parasitic liverwort: Aneura mirabilis. Arch Bryol 196: 1-4.

Shanker A. 2014a. Computational mining of microsatellites in the chloroplast genome of Ptilidium pulcherrimum, a liverwort. Intl Jour Environ 3: 50-58. doi: 10.3126/ije.v3i3.11063

Shanker A. 2014b. Computationally mined microsatellites in chloroplast genome of Pellia endiviifolia. Arch Bryol 199: 1-5.

Shanker A. 2014c. Simple sequence repeats mining using computational approach in chloroplast genome of Marchantia polymorpha. Arctoa 23, 145-149.

Shanker A. 2015. An update on sequenced chloroplast genomes of Bryophytes. Plant Sci Today 2, 102-104. doi: 10.14719/pst.2015.2.4.143

Shanker A., A. Bhargava, R. Bajpai, S. Singh, S. Srivastava, and V. Sharma. 2007a. Bioinformatically mined simple sequence repeats in UniGene of Citrus sinensis. Sci Hort 113, 353-361. doi: 10.1016/j.scienta.2007.04.011

Shanker A., A.Singh and V. Sharma. 2007. In silico mining in expressed sequences of Neurospora crassa for identification and abundance of microsatellites. Microbiol Res 162, 250- 256.

Srivastava D. and A. Shanker. 2015a. In silico mining and analysis of simple sequence repeats inchloroplast genomes of order Rosales. Res Jour Bioinformatics 2: 1-9.

Srivastava D. and A. Shanker. 2015b. Identification of simple sequence repeats in chloroplast genomes of Magnoliids through bioinformatics approach. Interdiscip Sci Comput Life Sci. doi 10.1007/s12539-015-0129-4.

Varshney R. K., T. Thiel, N. Stein, P. Langridge and A. Graner. 2002. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell & Mol Biol Lett 7: 537-546.

Downloads

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 Mar. 19];3(2):207-10. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/206

Issue

Section

Special Section: New Frontiers in Cryptogamic Botany

Similar Articles

You may also start an advanced similarity search for this article.