Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange

Abstract

BackgroundIn plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated gene silencing pathways play vital roles in plant development. Here, we used a high-throughput sequencing approach to characterize the miRNAs and their targeted transcripts in the leaf, flower and fruit of sweet orange.ResultsA total of 183 known miRNAs and 38 novel miRNAs were identified. An in-house script was used to identify all potential secondary siRNAs derived from miRNA-targeted transcripts using sRNA and degradome sequencing data. Genome mapping revealed that these miRNAs were evenly distributed across the genome with several small clusters, and 69 pre-miRNAs were co-localized with simple sequence repeats (SSRs). Noticeably, the loop size of pre-miR396c was influenced by the repeat number of CUU unit. The expression pattern of miRNAs among different tissues and developmental stages were further investigated by both qRT-PCR and RNA gel blotting. Interestingly, Csi-miR164 was highly expressed in fruit ripening stage, and was validated to target a NAC transcription factor. This study depicts a global picture of miRNAs and their target genes in the genome of sweet orange, and focused on the comparison among leaf, flower and fruit tissues.ConclusionsThis study provides a global view of miRNAs and their target genes in different tissue of sweet orange, and focused on the identification of miRNA involved in the regulation of fruit ripening. The results of this study lay a foundation for unraveling key regulators of orange fruit development and ripening on post-transcriptional level.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-695) contains supplementary material, which is available to authorized users.

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

“…miRNAs are small regulatory RNAs that play crucial roles in diverse aspects of plant development [54]. Identifying miRNA target genes is a fundamental step in determining the biological function for miRNAs.…”

Effect of Constitutive miR164 Expression on Plant Morphology and Fruit Development in Arabidopsis and Tomato

“…Furthermore, it has been observed that miR164 is also involved in senescence of leaves in Arabidopsis [13,41]. In addition, interestingly, miR164 is one of the most abundant miRNAs in some fruits such as orange [42], grape [43,44], tomato [45], and prickly pear fruit (tuna) [46]. In orange, it was observed that miR164 has remarkably higher expression in fruits in comparison with other organs [42].…”

“…In addition, interestingly, miR164 is one of the most abundant miRNAs in some fruits such as orange [42], grape [43,44], tomato [45], and prickly pear fruit (tuna) [46]. In orange, it was observed that miR164 has remarkably higher expression in fruits in comparison with other organs [42]. Moreover, miR164 accumulates to high levels during fruit ripening [42,45,46].…”

“…In orange, it was observed that miR164 has remarkably higher expression in fruits in comparison with other organs [42]. Moreover, miR164 accumulates to high levels during fruit ripening [42,45,46]. Therefore, in this work we studied the effect of miR164 overexpression in the reproductive phase and the process of fruit development, besides general plant development, in transgenic 35S::miR164 Arabidopsis and tomato plants.…”

Identification and characterization of genes involved in metabolism of n5 monoene precursors to n5 anacardic acids in the trichomes of Pelargonium x hortorum.

“…Other noteworthy miRNA candidates identified only in trichomes were miR-3954 which targets triose phosphate transporter gene required for metabolism and initiates siRNA biosynthesis [191][192][193] and miR-6483 which targets transmembrane proteins and regulates transport of cellular materials across the membrane 191,192,194 . To facilitate further studies of UMFA and AnAc synthesis in trichomes potential targets was uncovered.…”