Dataset Information

Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome.

ABSTRACT: BACKGROUND:The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations, making them particularly attractive to animals and humans. In olive drupes, including 'Cassanese' ones, ripening is usually accompanied by progressive chromatic change, resulting in a final red-brown colourization of both epidermis and mesocarp. This event has an exception in the 'Leucocarpa', in which we observed the destabilization in the equilibrium between the chlorophyll metabolism and that of the other pigments, particularly the anthocyanins, whose switch-off during maturation promotes the white colouration of the fruits. Recently, transcription profiling of 'Leucocarpa' and 'Cassanese' olives along ripening, performed through an Illumina RNA-seq approach, has provided useful insights on genes functions involved in fruit maturation such as those related to the biosynthesis of flavonoids and anthocyanins. METHODOLOGY:To assess expression alterations of genes involved in flavonoids and anthocyanins biosynthetic pathways during ripening, possibly caused by small nuclear RNA (snRNA) in olive drupes, snRNA libraries from 'Leucocarpa' and 'Cassanese' were constructed with RNAs extracted at 100 and 130 Days After Flowering (DAF) and sequenced by an Illumina approach. 130 conserved microRNAs (miRNA) in the Viridiplantae belonging to 14 miRNA families were identified. Regarding the 130 conserved miRNAs, approximately the 48% were identified in all libraries, 5 and 18 miRNAs were shared between the "Cassanese" (C100, C130) and "Leucocarpa" (L100, L130) libraries, respectively. CONCLUSION:For the remaining reads not-matching with known miRNAs in the Viridiplantae, we combined secondary structure and minimum free energy to discover novel olive miRNAs. Based on these analyses, 492 sequences were considered as putative novel miRNAs. The putative target genes of identified miRNA were computationally predicted by alignment with the olive drupe transcripts obtained from the same samples. A total of 218 transcripts were predicted as targets of 130 known and 492 putative novel miRNAs. Interestingly, some identified target genes are involved in negative regulation of anthocyanin metabolic process. Quantification of the expression pattern of three miRNA and their target transcripts by qRT-PCR assay confirmed the results of Illumina sequencing.

SUBMITTER: Carbone F

PROVIDER: S-EPMC6705801 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome.

Carbone Fabrizio F Bruno Leonardo L Perrotta Gaetano G Bitonti Maria B MB Muzzalupo Innocenzo I Chiappetta Adriana A

PloS one 20190822 8

<h4>Background</h4>The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations, making them particularly attractive to animals and humans. In olive drupes, including 'Cassanese' ones, ripening is usually accompanied by progressive chromatic change, resulting in a final red-brown colourization of both epidermis and mesocarp. This event has an exception in the 'Leucocarpa', in which we observed the destabilization in the equilibrium between the chloro ...[more]

PMID: 31437230

Similar Datasets

Project description:The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations making them particularly attractive to animals and humans. Usually, there is a progressive chromatic change characterized by a final red-brown color of both epidermis and mesocarp. This event has an exception in the ‘Leucocarpa’ cultivar, in which we observed the destabilization in the equilibrium between the metabolism on chlorophyll and that of the other pigments, particularly the anthocyanins, whose switch-off during maturation promotes the white coloration of the fruits. Recently, transcription profiling of ripening olives from ‘Leucocarpa’ and ‘Cassanese’ cultivars, through an Illumina RNA-seq approach, has provided some information about genes involved in fruit maturation as flavonid and anthocyanin transcripts. To study the possible gene differences involved in flavonoids and anthocyanins biosynthetic pathways during ripening possibly caused by small nuclear RNA (snRNA) in olive drupes, the snRNA libraries of fruit ripening from ‘Leucocarpa’ and ‘Cassanese’ were constructed with RNAs from drupes at 100 and 130 DAF (Days After Flowering) and sequenced by Illumina approach. Comparing sequence information, 130 conserved microRNAs (miRNA) in the Viridiplantae were detected belonging 14 miRNA families. For the remaining read not-matched with known miRNAs in the Viridiplantae, we combined secondary structure and minimum free energy to discover novel olive miRNAs. Based on these analyses, 492 miRNAs were considered as putative novel. To increase insights into the functions of known and putative novel miRNA in olive, putative target genes were computationally predicted by alignment with the olive drupe transcripts obtained from the same samples. A total of 32 and 186 transcripts were predicted as targets of 130 known and 492 putative novel miRNA, respectively. The identified target genes are involved in a broad range of biological processes. Interestingly, some genes involved in negative regulation of anthocyanin metabolic process, were identified as target of miR168 suggesting that this miRNA family is likely operative during color transition in olive.

Project description:BackgroundAlternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the following year ("off-year"). Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA), being gene-expression regulators that have been found to be involved as key determinants in several physiological processes.ResultsSix olive (Olea europaea L. cv. Ayvalik variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on year" and "off year" leaves in July and in November, respectively) and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways.ConclusionA comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also provide significant data on the miRNA-fruit development interaction and advance perspectives in the miRNA profile of the olive tree.

Project description:In the olive (Olea europaea L.), an economically leading oil crop worldwide, fruit size and yield are determined by the early stages of fruit development. However, few detailed analyses of this stage of fruit development are available. This study offers an extensive characterization of the various processes involved in early olive fruit growth (cell division, cell cycle regulation, and cell expansion). For this, cytological, hormonal, and transcriptional changes characterizing the phases of early fruit development were analyzed in olive fruit of the cv. 'Picual'. First, the surface area and mitotic activity (by flow cytometry) of fruit cells were investigated during early olive fruit development, from 0 to 42 days post-anthesis (DPA). The results demonstrate that the cell division phase extends up to 21 DPA, during which the maximal proportion of 4C cells in olive fruits was reached at 14 DPA, indicating that intensive cell division was activated in olive fruits at that time. Subsequently, fruit cell expansion lasted as long as 3 weeks more before endocarp lignification. Finally, the molecular mechanisms controlling the early fruit development were investigated by analyzing the transcriptome of olive flowers at anthesis (fruit set) as well as olive fruits at 14 DPA (cell division phase) and at 28 DPA (cell expansion phase). Sequential induction of the cell cycle regulating genes is associated with the upregulation of genes involved in cell wall remodeling and ion fluxes, and with a shift in plant hormone metabolism and signaling genes during early olive fruit development. This occurs together with transcriptional activity of subtilisin-like protease proteins together with transcription factors potentially involved in early fruit growth signaling. This gene expression profile, together with hormonal regulators, offers new insights for understanding the processes that regulate cell division and expansion, and ultimately fruit yield and olive size.

Dataset Information

Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome.

Publications

Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets