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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

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Author(s):
Zanca, Almir S. [1] ; Vicentini, Renato [1] ; Ortiz-Morea, Fausto A. [2] ; Del Bem, Luiz E. V. [1] ; da Silva, Marcio J. [1] ; Vincentz, Michel [1, 3] ; Nogueira, Fabio T. S. [2, 4]
Total Authors: 7
Affiliation:
[1] Univ Estadual Campinas, CBMEG, Campinas, SP - Brazil
[2] ESALQ USP, Ctr Biotecnol Agr CEBTEC, Escola Super Agr Luiz de Queiroz, Piracicaba, SP - Brazil
[3] Univ Estadual Campinas, Dept Biol Vegetal, Inst Biol, Campinas, SP - Brazil
[4] Univ Estadual Paulista UNESP, Dept Genet, Inst Biociencias, Botucatu, SP - Brazil
Total Affiliations: 4
Document type: Journal article
Source: BMC PLANT BIOLOGY; v. 10, NOV 24 2010.
Web of Science Citations: 47
Abstract

Background: MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species. Results: In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots. Conclusions: Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms. (AU)