Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq study on root samples from Olea europaea cultivars

ABSTRACT: 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.

ORGANISM(S): Olea europaea

PROVIDER: GSE152236 | GEO | 2021/04/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide identification of alternate bearing-associated miRNA in the olive tree (Olea europaea)

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

microarray_VD

Project description:The soilborne fungus, Verticillium dahliae, causes Verticillium wilt disease in plants. Verticillium wilt is difficult to control since V. dahliae is capable of persisting in the soil for 10 to15 years as melanized microsclerotia, rendering crop rotation strategies for disease control ineffective. Microsclerotia of V. dahliae overwinter and germinate to produce infectious hyphae that give rise to primary infections. Consequentially, microsclerotia formation, maintenance, and germination are critically important processes in the disease cycle of V. dahliae.

2013-09-06 | E-MTAB-1793 | biostudies-arrayexpress

Genome-wide identification of alternate bearing-associated miRNA in the olive tree (Olea europaea)

2012-12-18 | GSE42978 | GEO

Proteo-metabolomic study of olive (cv. ‘Chondrolia Chalkidikis’) drupe development and maturation

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

RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae

Project description:Verticillium dahliae is a soilborne fungus that causes wilt disease in plants. The microsclerotia of V. dahliae produce infectious hyphae that give rise to primary infections. In this study, RNA-seq libraries were prepared from microsclerotia (MS)-producing cultures of V. dahliae (ave = 52.23 million reads), and those not producing microsclerotia (NoMS, ave = 50.58 million reads) and analyzed for differential gene expression.

2013-09-06 | E-MTAB-1581 | biostudies-arrayexpress

Transcriptome and metabolome profiling reveals key pathways and metabolites involved in defense response of upland cotton against Verticillium dahliae

Project description:Cotton is the main source of natural fiber in the textile industry, making it one of the most economically important fiber crops in the world. Verticillium wilt, caused by the pathogenic fungus Verticillium dahlia, is one of the most damaging biotic factors limiting cotton production. Mechanistic details of cotton defense responses to verticillium wilt remain unclear. In this study, GFP-labeled strain of V. dahlia was used to track colonization in cotton roots, and clear conidial germination could be observed at 48 hours post-inoculation (hpi), marking this as a crucial time point during infection. Transcriptome analysis identified 1,523 and 8,270 differentially expressed genes (DEGs) at 24 hpi and 48 hpi, respectively. Metabolomic screening found 78 differentially accumulated metabolites (DAMs) at 48 hpi. Conjoint analysis indicated that the phenylpropanoid biosynthesis pathway was activated in cotton infected with V. dahliae. The five metabolites in the phenylpropanoid biosynthesis pathway, including caffeic acid, coniferyl alcohol, coniferin, scopoletin and scopolin, could significantly inhibit V. dahlia growth in vitro, implicating their roles in cotton resistance to Verticillium wilt. The findings expand our understanding of molecular mechanisms underlying the pathogen defense response against V. dahlia infection in upland cotton, which may lead to future insights into controlling Verticillium wilt disease.

2023-12-26 | GSE221845 | GEO

Gene expression pattern in olive tree organs (Olea europaea L.)

Project description:Gene expression pattern in olive tree organs (Olea europaea L.)

| PRJNA590386 | ENA

Verticillium dahliae-Arabidopsis interaction causes changes in gene expression profiles and jasmonate levels on different time scales

Project description:Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 hours induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense and stress responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.

2018-02-08 | GSE104590 | GEO

Transcriptome sequencing of Verticillium dahliae and △VdBre1 mutant

Project description:The soil-borne ascomycete Verticillium dahliae which causes wilt disease in many important crops results a severe reduction in crop yield and quality. During infection, the V.dahliae will secrete a lot of secondary metabolites which act as toxic factors to promote the infection process. However, the mechanism underlying how V.dahliae secondary metabolites regulate cotton infection remains largely unexplored. BRE1 is a highly conserved ubiquitin ligase (E3) enzymes and regulate expression of specific genes related to the production of secondary metabolites. To get an insight into the genes regulated by VdBre1, the comparative transcriptomic analysis was conducted between VdBre1 deletion mutant and the wild type V592. The conidia of wilde type and mutant were collected and total RNA was extracted using fungal RNA kit, sequencing was performed on an BGISEQ-500 platform.

2021-05-20 | GSE151401 | GEO

Study on the infection mechanism of Verticillium dahliae on potato regulated by the viruence-related pigment biosynthesis protein Vayg1

Project description:Verticillium wilt of potato caused by Verticillium dahliae, also called potato early dying disease, is an important factor limiting potato production in the world. Currently, the poor understanding of the pathogenic mechanism of Verticillium dahliae has led to increasingly severe challenges in the effective control of Verticillium wilt. Many studies have shown that pigment biosynthesis related proteins are virulence factors of Verticillium dahliae, while the regulatory mechanisms are still unknown. In order to elucidate the pathogenic mechanism regulated by the virulence related pigment biosynthesis protein Vayg1 in Verticillium dahliae, proteomic analysis will be used to judge the Vayg1 deletion mutant and the wild-type strain during the infection of potato to explore the Vayg1 involved pathogenic protein network, aiming to identify and understand relevant pathogenic pathways to provide an important support for deeper understanding of the pathogenic mechanism of the pathogen. The key proteins related to virulence and molecular networks that will be obtained in this study could provide new targets for the control of Verticillium wilt and new insights for the improvement of disease management.

2023-02-15 | PXD040131 |

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data