Computational Identification of Conserved microRNAs and Their Targets in Tea (Camellia sinensis)

Akan Das,Tapan Kumar Mondal

doi:10.4236/ajps.2010.12010

Abstract

MicroRNAs (miRNAs) are a class of ~22 nucleotides long non coding RNA molecules which play an important role in gene regulation at the post transcriptional level. The conserved nature of miRNAs provides the basis of new miRNA identification through homology search. In an attempt to identify new conserved miRNAs in tea, previously known plant miRNAs were used for searching their homolog in a tea Expressed Sequence Tags and full length nucleotide sequence database. The sequences showing homolog no more than four mismatches were predicted for their fold back structures and passed through a series of filtration criteria, finally led us to identify 13 conserved miRNAs in tea belonging to 9 miRNA families. A total of 37 potential target genes in Arabidopsis were identified subsequently for 7 miRNA families based on their sequence complementarity which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%). Overall, our findings will accelerate the way for further researches of miRNAs and their functions in tea.

Highlights

MicroRNAs are short (~22 nt), endogenous non coding RNAs that play an important role in many biological processes [1]
A total of 37 potential target genes in Arabidopsis were identified subsequently for 7 miRNA families based on their sequence complementarity which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%)
A total of 14,819 sequences containing 2,023 full length nucleotides and 12,796 Expressed Sequence Tags (ESTs) were obtained from GenBank

Summary

Introduction

MicroRNAs (miRNAs) are short (~22 nt), endogenous non coding RNAs that play an important role in many biological processes [1]. MiRNAs are involved in diverse aspects of plant growth and development such as leaf morphology and polarity, root formation, transition from juvenile to adult vegetative phase and vegetative to flowering phase, flowering time, floral organ identity and reproduction [5, 6]. They are found to be involved in response to pathogen invasion [7], hormone signaling [8,9], environmental stress [10,11] and promotion of anti-viral defence [12]. EST analysis makes it possible for studying conserved miRNAs and their functions in species whose genome sequences have not been well known [10,18,19]

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Conclusion