Title

In silico mining of SSR markers from Expressed Sequence Tags of bamboo species 

Authors

Oviya Iyappan Ramalakshmi ^{1, *}, Shanmughavel Piramanayagam²

Affiliation

¹Research Scholar, Department of Bioinformatics, Bharathiar University, Coimbatore- 641046, India; ²Assistant Professor, Department of Bioinformatics, Bharathiar University, Coimbatore- 641046, India 

Email

iroviya@yahoo.co.in

+91-422-2422265

+91-422-2422387; * Corresponding author

Article Type

Hypothesis

Date

Received September 08, 2010; Accepted October 11, 2010; Published November 27, 2010
 

With the ever increasing number of Expressed Sequence Tags (ESTs) from various sequencing projects, ESTs have become valuable and first-hand source of in-silico mining of simple sequence repeats (SSR) markers. We examined a total of 3419 EST sequences from three bamboo species, namely, Phyllostachys edulis, Bambusa oldhamii and Dendrocalamus sinicus for the presence of di- to hexa- microsatellites. The frequency of SSR containing ESTs varied from 5.36% in B. oldhamii to 13.05% in P. edulis. No SSRs were found in D. sinicus. Tri-nucleotide repeats (49.34%) were most frequent in P. edulis, while not much comparable difference in repeats was found in B. oldhamii. Flanking primer pairs were also designed in-silico for the sequences containing SSRs and their position on the genome hypothesized using similarity searching. SSRs located in open reading frame (ORF) were given functional annotation using Gene Ontology. Polymorphic SSRs were also detected using new pipeline- polySSR. Polymorphism level was very low (2.43%) and the position of the polymorphic SSRs was determined. The development of SSRs and the study of polymorphism will help in the further study of intra- and inter- gene flow, genetic structure, variability, linkage mapping and evolutionary relationships in bamboo. 

Keywords

Expressed Sequence Tags (EST), Simple Sequence Repeats (SSR), bamboo, Phyllostachys edulis, Bambusa oldhamii, and Dendrocalamus sinicus.

Citation

Oviya & Shanmughavel. Bioinformation, 5(6): 240-243, 2010

Edited by

Susmita Datta

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.