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Title

 

 

 

 

Exploiting EST databases for the mining and characterization of short sequence repeat (SSR) markers in Catharanthus roseus L. 

Authors

Raj Kumar Joshi, Basudeba Kar, Sanghamitra Nayak*

Affiliation

Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India 

Email

sanghamitran@yahoo.com; *Corresponding author  

Phone

09437061976

Article Type

Hypothesis

 

Date

Received January 05, 2011; Accepted January 06, 2011; Published February 07, 2011
 

Abstract

Periwinkle (Catharanthus roseus L.) (Family: Apocyanaceae) is a ornamental plants with great medicinal properties. Although it is represented by seven species, little work has been carried out on its genetic characterization due to non-availability of reliable molecular markers. Simple sequence repeats (SSRs) have been widely applied as molecular markers in genetic studies. With the rapid increase in the deposition of nucleotide sequences in the public databases and advent of bioinformatics tools, it has become a cost effective and fast approach to scan for microsatellite repeats and exploit the possibility of converting it into potential genetic markers. Expressed sequence tags (ESTís) from Catharanthus roseus were used for the screening of Class I (hyper variable) simple sequence repeats (SSRís). A total of 502 microsatellite repeats were detected from 21730 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs account to 1 SSR per 10.21 kb of EST. Mononucleotides was the most abundant class of microsatellite motifs. It accounted for 44.02% of the total, followed by the trinucleotide (26.09%) and dinucleotide repeats (14.34%). Among all the repeat motifs, (A/T)n accounted for the highest Proportion (36.25%) followed by (AAG)n. These detected SSRs can be used to design primers that have functional importance and should also facilitate the analysis of genetic diversity, variability, linkage mapping and evolutionary relationships in plants especially medicinal plants.  

Keywords

Catharanthus roseus, Expresses sequence tags, short sequence repeats, SSR Locator.

Citation

Joshi et al. Bioinformation 5(9): 378-381 (2011)

Edited by

P Kangueane

 

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.