In silico microRNA identification from paprika (Capsicum annuum) ESTs

T. M. Manila1, A. Riju1, K. Lakshmi Priya Darshini1, A. Chandrasekar1 & S. J. Eapen1

Indian Institute of Spices Research, Calicut 673012, Kerala, India.

Abstract
A total of 33,311 Expressed Sequence Tags (EST) of paprika were mined from the GenBank EST database. The redundancy of the EST sequences was removed using CAP3 and it resulted 4,541 contigs 8,539 singletons as nonredundant data sets. The microRNAs were predicted using the program miRNAfinder. This program predicted a total of 85 miRNAs miRNAs. Another study was carried out to find the homologes miRNA using blast based tool named “miRseeK’ A total of 13 miRNAs with significant similarity with the plant miRNAs were obtained from paprika ESTs. The targets of the predicted miRNAs were found using the program miRU2. Findings suggest that most miRNAs play an important role in plant development, signal transduction, protein degradation and in response to environmental stress. The miRNAs were found to be perfectly or nearly complementary to its target mRNAs.

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