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New Insights on Coffea miRNAs: Features and Evolutionary Conservation

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Abstract

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.

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Acknowledgments

The authors thank the Laboratory of Plant Molecular Physiology (LFMP) of the Federal University of Lavras (UFLA), the National Council for Scientific and Technological Development (CNPq) for the fellowships granted, the Minas Gerais Research Foundation (FAPEMIG), and National Institute for Science and Technology for Coffee (INCT-Café) for funding this work and the Coordination of Improvement of Higher Education (CAPES) for grants.

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Chaves, S.S., Fernandes-Brum, C.N., Silva, G.F.F. et al. New Insights on Coffea miRNAs: Features and Evolutionary Conservation. Appl Biochem Biotechnol 177, 879–908 (2015). https://doi.org/10.1007/s12010-015-1785-x

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