title: Computational identification and comparative analysis of miRNA precursors in three palm species.
abstract: In the present study, miRNA precursors in the genomes of three palm species were identified. Analyzes of sequence conservation and biological function of their putative targets contribute to understand the roles of miRNA in palm biology. MicroRNAs are small RNAs of 20-25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.
authors.affiliation: Universidade Federal Rural da Amazonia, Belém, Brazil.|Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
authors.forename: Aline Cunha
authors.initials: AC
authors.lastname: da Silva
authors.affiliation: Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, 2000, P5-227A, Parque Califórnia, Campos dos Goytacazes, RJ, 28013-602, Brazil.
authors.forename: Clícia
authors.initials: C
authors.lastname: Grativol
authors.affiliation: Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
authors.forename: Flávia
authors.initials: F
authors.lastname: Thiebaut
authors.affiliation: Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
authors.forename: Adriana Silva
authors.initials: AS
authors.lastname: Hemerly
authors.affiliation: Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil. paulof@bioqmed.ufrj.br.
authors.forename: Paulo Cavalcanti Gomes
authors.initials: PC
authors.lastname: Ferreira
mesh_terms: D028023:Arecaceae / Q000235:genetics*; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs; D028521:Musa / Q000235:genetics; D065749:Phoeniceae / Q000235:genetics; D012322:RNA Precursors; D018749:RNA, Plant
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant
keywords: In silico analysis; Palm genome; Small RNAs; Target genes