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Deep sequencing of olive (Olea europaea l.) Short RNAs identifies microRNAs targeting involved in drupe ripening

ABSTRACT: 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.

ORGANISM(S): Olea europaea

PROVIDER: GSE104763 | GEO | 2019/08/11

REPOSITORIES: GEO

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Project description:Pink-flowered strawberry is a new promising ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, prolonged flowering period and edible fruits. However, the transcriptional events underlying anthocyanins biosynthesis pathway have not been fully characterized in its petal coloration. The pigment compounds accumulated in its fruits were the same as cultivated strawberry, but different from in its flowers. To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed an integrated analyses of the transcriptome and metabolomes involved in red petals at three development stages (Bud stage (L), Coloration beginning stage (Z) and Big bud stage (D)) of pink-flowered strawberry. Transcript and metabolite profiles were generated through high-throughput RNA-sequencing and high-performance liquid chromatography coupled with mass spectrometry, respectively. The results showed that the main pigments of red and dark pink petals were anthocyanins, among which cyanidins were the main compounds. There were no anthocyanins detected in white-flowered hybrids. A total of 50 285 non-redundant unigenes were obtained from the transcriptome databases, among which 59 differentially expressed genes could be identified as putative homologues of flower coloration related genes. Based on a comprehensive analysis relating pigmentation compounds to gene expression profiles, the mechanism of flower color formation was examined in pink-flowered strawberry. Furthermore, a new hypothesis explaining the lack of color phenotype of the white-flowered strawberry hybrids from the level of the transcriptome. The expression patterns of FpDFR gene and FpANS gene corresponded to the accumulation patterns of cyanidin contents in pink-flowered strawberry hybrids with different shades of pink; Whereas other anthocyanin biosynthesis genes were weakly related flower color deepened. Moreover, FpANS, FpBZ1 and FpUGT75C1 genes were the key factors that lead to the inability to accumulate anthocyanins in the white petals of PFS hybrids. Meanwhile, the competitive effect of FpFLS gene and FpDFR gene may further inhibit anthocyanin synthesis. The data presented herein are important for understanding of the molecular mechanisms underlying the petal pigmentation and will be powerful for integrating into novel genes that are potential targets for breeding new valuable pink-flowered strawberry cultivars.

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Deep sequencing of olive (Olea europaea l.) Short RNAs identifies microRNAs targeting involved in drupe ripening

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