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Open Access Highly Accessed Research article

Computational identification and analysis of novel sugarcane microRNAs

Flávia Thiebaut1, Clícia Grativol1, Mariana Carnavale-Bottino1, Cristian Antonio Rojas2, Milos Tanurdzic4, Laurent Farinelli5, Robert A Martienssen3, Adriana Silva Hemerly1 and Paulo Cavalcanti Gomes Ferreira1*

Author Affiliations

1 Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rua Rodolpho Paulo Rocco s/n°, CCS, Bl.B-33A, Cidade Universitária 21941-590, Rio de Janeiro, RJ, Brazil

2 Universidade Federal da Integração Latino-Americana, Av. Tancredo Neves, 6731, Bl.4, 85867-970, Foz do Iguaçu, PR, Brazil

3 Cold Spring Harbor Laboratory, 1 Bungtown RD, Cold Spring Harbor, NY, 11724, USA

4 School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia

5 Fasteris SA, 1228-Plan-les-Ouates, Switzerland

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BMC Genomics 2012, 13:290  doi:10.1186/1471-2164-13-290

Published: 2 July 2012

Abstract

Background

MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology.

Results

A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively.

Conclusions

A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.

Keywords:
Small RNA; Biotic stress; Abiotic stress; Deep sequencing