New Insights on Coffea miRNAs: Features and Evolutionary Conservation.
Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.
Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil.
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Chaves
Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil.
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Fernandes-Brum
Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil.
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Silva
Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil.
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Ferrara-Barbosa
Central Laboratory of Molecular Biology (LCBM), Chemistry Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil.
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Paiva
Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil.
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Nogueira
Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil.
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Cardoso
Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil.
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Amaral
Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil.
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de Souza Gomes
Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil. chalfunjunior@dbi.ufla.br.
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http://orcid.org/0000-0002-1794-9429
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Chalfun-Junior
D001483:Base Sequence; D040503:Coffea / Q000235:genetics* / Q000502:physiology; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D023281:Genomics; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013312:Stress, Physiological
D035683:MicroRNAs
5′ RACE; Coffee; Evolutionary conservation; MicroRNAs; PsRNATarget; Stem-loop RT-PCR