Computational identification and analysis of novel sugarcane microRNAs

BMC Genomics

Research Article

Robert A Martienssen¹  Laurent Farinelli²  Paulo Cavalcanti Gomes Ferreira³  Adriana Silva Hemerly³  Clícia Grativol³  Mariana Carnavale-Bottino³  Flávia Thiebaut³  Milos Tanurdzic⁴  Cristian Antonio Rojas⁵ 

[1] Cold Spring Harbor Laboratory, 1 Bungtown RD, 11724, Cold Spring Harbor, NY, USA;Fasteris SA, 1228-Plan-les-Ouates, Switzerland;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;School of Biological Sciences, The University of Queensland, 4072, St Lucia, QLD, Australia;Universidade Federal da Integração Latino-Americana, Av. Tancredo Neves, 6731, Bl.4, 85867-970, Foz do Iguaçu, PR, Brazil;

关键词: Small RNA;    Biotic stress;    Abiotic stress;    Deep sequencing;   

DOI  :  10.1186/1471-2164-13-290

 received in 2012-01-02, accepted in 2012-05-02,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundMicroRNA-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.ResultsA 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.ConclusionsA 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.

【 授权许可】

Unknown   
© Thiebaut et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.