Ontology highlight
ABSTRACT:
PROVIDER: PRJEB13716 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1370920.fastq.gz | Fastqsanger.gz | |||
| ERR1370921.fastq.gz | Fastqsanger.gz | |||
| ERR1370922.fastq.gz | Fastqsanger.gz | |||
| ERR1370923.fastq.gz | Fastqsanger.gz | |||
| ERR1370924.fastq.gz | Fastqsanger.gz |
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Project description:We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples. Sequences of six olive miRNAs (Olea europaea L. )(Ayvalık variety) plants (ripe and unripe fruits, leaves of mature and juvenile plants of both "on-year" and "off-year") were generated by Illumina sequencing
2012-12-18 | E-GEOD-42978 | biostudies-arrayexpress
Project description:We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples.
2012-12-18 | GSE42978 | GEO
Project description:Cultivated olive tree (Olea europaea L. subsp. europaea var. europaea) is one of most relevant worldwide-extended crops. Since this plant has a huge effect on the economy of several regions, especially in those located in the Mediterranean basin, all efforts focused on its protection have a great relevance in agriculture sustainability. As all extended crops, olive tree cultivars are under the threat of a wide range of pathogens. Among them, Verticillium dahliae has been in the spotlight in the last decades because the disease caused by this soil-borne fungus (Verticillium wilt) is easily spread and can eventually kill the tree. In this line, many different factors have been studied in order to shed some light on the molecular/genetic mechanisms underlying the Olea europaea-Verticillium dahliae interaction, some of them focused on the gene expression pattern of the host. In this study, the expression pattern of roots from thirty-six O. europaea cultivars with different resistance/susceptibility degree to Verticillium wilt has been analyzed by RNA-Seq. As a result, processes involved in plant defense, transcription and root development have emerged as potential players in the differential response to Verticillium wilt of these cultivars. Additionally, a quite interesting set of 421 genes with an opposite expression pattern in those cultivars showing extreme resistance/susceptibility to Verticillium wilt has been discovered, establishing a solid group of candidates to take into account in future genetic improvement programs.
2021-04-07 | GSE152236 | GEO
Project description:Gene expression pattern in olive tree organs (Olea europaea L.)
| PRJNA590386 | ENA
Project description:Olive (Olea europaea L.) is one of the most economically relevant tree crops in the Mediterranean basin. In this study, a comparative proteomic along with metabolomic-wide investigation was carried out on drupes of Greek olive cultivar 'Chondrolia Chalkidikis', collected across six developmental stages (S), namely seed development (S1, S2), mesocarp development (S3, S4, S5) and full maturation (S6). These stages were first characterized through the dynamics of fruit weight, dimensions and color parameters such as lightness, redness and yellowness. Combined gas chromatography–mass spectrometry and reversed–phase liquid chromatography quadrupole–time–of–flight mass spectrometry (RPLC–QToF–MS) procedures quantified 47 primary (e.g. allose, galactose, quinic acid, sorbitol, stearic acid) and 21 secondary (e.g. elenolic acid, oleacin, rutin, luteolin, hydroxytyrosol) metabolites in mesocarp samples during development. Protein analysis via nano–LC coupled to HDAM Orbitrap mass spectrometer, identified 3258 proteins from which the 350 were differentially accumulated between the final maturation stages (S5 and S6). Olive genome-based functional annotation showed that the largest proportion of identified proteins were involved in primary metabolism [i.e. lipoxygenases (LOX1/5)], energy [i.e. ferredoxin NADP+ reductase (FNR)], signal transduction [i.e. serine/threonine kinases (SAPK2, SRK2A, STK), transcription [i.e. elongation factor 2 (EEF2)] and protein destination [i.e. serine carboxypeptidase (SCPL)]. This investigation provides a reference framework for further nutritional and breeding studies, also allowing cross comparison among other olive cultivars.
2021-11-25 | PXD021086 | Pride
Project description:Small RNAs of 20 to 25 nucleotides in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the small RNA component of more than 40 plant species. Here, use deep sequencing and molecular methods to report the first inventory of small RNAs in olive (Olea europaea). Small RNAs of 24 nts dominate the small RNA transcriptome and atypically accumulate to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. By contrast, small RNAs of 20 to 22 nts were poorly represented in the population at levels lower than those found in most plant species tested. A total of 14 known miRNA families were identified in two libraries prepared from growing and dormant lateral buds. We found that some known miRNAs showed tissue- and/or developmental-specific expression. Also, seven novel, olive-specific miRNA candidates were found in our sequenced set of which 1 were supported by their star strands. Potential precursors for these miRNA candidates with intramolecular folding capacities were found in the olive EST database. Target mRNAs of conserved miRNAs and new olive-specific miRNA were computationally predicted among the olive EST collection and experimentally validated through endonucleolytic cleavage assays.
2011-03-31 | GSE27093 | GEO
Project description:Small RNAs of 20 to 25 nucleotides in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the small RNA component of more than 40 plant species. Here, use deep sequencing and molecular methods to report the first inventory of small RNAs in olive (Olea europaea). Small RNAs of 24 nts dominate the small RNA transcriptome and atypically accumulate to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. By contrast, small RNAs of 20 to 22 nts were poorly represented in the population at levels lower than those found in most plant species tested. A total of 14 known miRNA families were identified in two libraries prepared from growing and dormant lateral buds. We found that some known miRNAs showed tissue- and/or developmental-specific expression. Also, seven novel, olive-specific miRNA candidates were found in our sequenced set of which 1 were supported by their star strands. Potential precursors for these miRNA candidates with intramolecular folding capacities were found in the olive EST database. Target mRNAs of conserved miRNAs and new olive-specific miRNA were computationally predicted among the olive EST collection and experimentally validated through endonucleolytic cleavage assays. Two samples analyzed: growing (juvenile) and dormant (adult) lateral buds from the progeny of a genetic cross between the Picual and Arbequina olive varieties
2011-03-31 | E-GEOD-27093 | biostudies-arrayexpress
Project description:Purpose: Nonstructural carbohydrates has a major impact on trees response to meteorological conditions. The goals of this study were to define which changes in gene expression are linked to possible mechanisms used by the plant to buffer the decline in carbon source during gradual soil drying, an intensive abrupt heat wave, and recovery from drought? Methods: We combined measurements of nonstructural carbohydrates (NSC), tree physiology and expression of genes encoding starch metabolism enzymes. The experiment was conducted on potted olive (Olea europaea) trees, half of them under 28 days of soil drought. Results: We identified the gene family members relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase’s and starch synthase’s family members were identified, with some members upregulated throughout drought while other members in recovery. The daily starch metabolism machinery was different from the stress-mode starch metabolism machinery when some genes are unique to the stress-mode response.
2020-12-23 | GSE145100 | GEO