Olice cultivars resequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35540 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR3685180_1.fastq.gz | Fastqsanger.gz | |||
| ERR3685180_2.fastq.gz | Fastqsanger.gz | |||
| ERR3686560_1.fastq.gz | Fastqsanger.gz | |||
| ERR3686560_2.fastq.gz | Fastqsanger.gz |
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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.
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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:Endophytic microbial community of olive trees (Olea europaea)
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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.
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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.
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Project description:Genetic changes involved in the juvenile-to-adult transition in the shoot apex of Olea europaea L. occurs years before the first flowering.
2013-11-09 | GSE52213 | GEO
Project description:Proteins and peptides are minor components of vegetal oils. The presence of these compounds in virgin olive oil was first reported in 2001, but the nature of the olive oil proteome is still a puzzling question for food science researchers. In this project, we have compiled for a first time a comprehensive proteomic dataset of olive fruit and fungal proteins that are present at low but measurable concentrations in a vegetable oil from a crop of great agronomical relevance as olive (Olea europaea L.). Accurate mass nLC-MS data were collected in high definition direct data analysis (HD-DDA) mode using the ion mobility separation step. Protein identification was performed using the Mascot Server v2.2.07 software (Matrix Science) against an ad hoc database made of olive protein entries. Starting from this proteomic record, the impact of these proteins on olive oil stability and quality could be tested. Moreover, the effect of olive oil proteins on human health and their potential use as functional food components could be also evaluated. In addition, this dataset provides a resource for use in further functional comparisons across other vegetable oils, and also expands the proteomic resources to non-model species, thus also allowing further comparative inter-species studies.
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