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Analysis of unigene derived microsatellite markers in family solanaceae



Sanchita Gupta1*, Kumar Parijat Tripathi2, Sudeep Roy1, Ashok Sharma1



1Biotechnology Division, Central Institute of Medicinal & Aromatic Plants (Council of Scientific & Industrial Research), Post Office CIMAP, Lucknow India; 2Institute for Evolution and Biodiversity, University of Münster, Germany;

E-mail*; * Corresponding author


Article Type





Received August 4, 2010; Accepted August 26, 2010; Published September 20, 2010



The family Solanaceae is the source of several economically important plants. The aim of this study was to trace and characterize simple sequence repeat (SSR) markers from unigene sequences of Solanum lycopersicum, an important member of family Solanaceae. 18,228 unigene sequences of Solanum lycopersicum was taken in order to develop SSR markers and analyzed for the in-silico design of PCR primers. A total of 12,090 (66.32 %) unigenes containing 17,524 SSRs (microsatellites) were identified. The average frequency of microsatellites in unigenes was one in every 1.3 kb of sequence. The analysis revealed that trinucleotide motifs, coding for Glutamic acid (GAA) and AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking sequences of the SSRs generated 877 primers with forward and reverse strands. Functional categorization of SSRs containing unigenes was done through gene ontology terms like Biological process, Cellular component and Molecular function.





Gupta et al. Bioinformation 5(3): 113-121 (2010)

Edited by


P. Kangueane








Biomedical Informatics




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.