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Title

Mining for SSRs and FDMs from expressed sequence tags of Camellia sinensis

 

Authors

Jagajjit Sahu, Ranjan Sarmah, Budheswar Dehury, Kishore Sarma, Smita Sahoo, Mousumi Sahu, Madhumita Barooah, Mahendra Kumar Modi & Priyabrata Sen *

 

Affiliation

Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, Assam, India

 

Email

pbsen14@yahoo.co.in; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received March 16, 2012; Accepted March 21, 2012; Published March 31, 2012

Abstract

Simple Sequence Repeats (SSRs) developed from Expressed Sequence Tags (ESTs), known as EST-SSRs are most widely used and potentially valuable source of gene based markers for their high levels of crosstaxon portability, rapid and less expensive development. The EST sequence information in the publicly available databases is increasing in a faster rate. The emerging computational approach provides a better alternative process of development of SSR markers from the ESTs than the conventional methods. In the present study, 12,851 EST sequences of Camellia sinensis, downloaded from National Center for Biotechnology Information (NCBI) were mined for the development of Microsatellites. 6148 (4779 singletons and 1369 contigs) non redundant EST sequences were found after preprocessing and assembly of these sequences using various computational tools. Out of total 3822.68 kb sequence examined, 1636 (26.61%) EST sequences containing 2371 SSRs were detected with a density of 1 SSR/1.61 kb leading to development of 245 primer pairs. These mined EST-SSR markers will help further in the study of variability, mapping, evolutionary relationship in Camellia sinensis. In addition, these developed SSRs can also be applied for various studies across species.

 

Keywords

Expressed Sequence Tags (ESTs), Simple Sequence Repeats (SSRs), Functional Domain Markers (FDM), Camellia sinensis.

Citation

Sahu et al. Bioinformation 8(6):260-266 (2012)
 

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.