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Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

ABSTRACT: Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

PROVIDER: PRJNA605710 | ENA |

REPOSITORIES: ENA

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Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

Project description:Drought is considered as a threat to the sustainability of Mediterranean forests and, of the agro-silvo-pastoral “dehesa” system. Holm oak (Quercus ilex L.) is one of the most representative species of these ecosystems and this abiotic stress causes a high tree mortality rate, being more accused at the seedling stage. In this study, an integrative analysis of transcriptome and proteome in leaves of Q. ilex seedlings under drought conditions was carried out to identify gene products involved in the metabolic pathways related to drought tolerant mechanisms.

2022-11-11 | PXD017493 | Pride

Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

Project description:Transcript profiling of leaves from Quercus ilex seedlings subjected to well-watering and drought-stress (irrigation withdrawal) conditions

2020-04-03 | GSE145009 | GEO

The Holm oak (Quercus ilex) proteome as defined by shotgun MS (nLC-MS/MS, Orbitrap) approach

Project description:Holm oak (Quercus ilex) is the most important and representative specie of the Mediterranean forest and of the Spanish agrosilvo-pastoral ecosystem “Dehesa”. Despite its environmental and economic interest, Holm oak is still an orphan species whose biology is very little known, especially at the molecular level. In this research, we have performed a shotgun proteomic approach (nLC-MSMS, Orbitrap) to analyze the Holm oak proteome, using, as starting material, a pool generated by mixing equal amounts of homogenized tissue, including embryo, cotyledons (from mature acorns), and leaves and roots (from 6-month old plantlets grown in a greenhouse under environmental conditions). The proteome generated will be the bases of further studies on population variability, growth, development and responses to stresses in this species.

2018-01-16 | PXD008001 | Pride

2-DE proteomics analysis of drought treated seedlings of Quercus ilex

Project description:Applying a gel-based proteomic approach, the dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and subjected to two-dimensional electrophoresis. Coomassie colloidal stained gel images were analysed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in the three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Taxonomy Holm oak (Quercus ilex subsp. Ballota [Desf.] Samp.). Dentro de Q. ilex hay dos subespecies, ilex ilex e ilex Ballota.

2015-09-09 | PXD002484 | Pride

Proteomics data analysis for the identification of proteins and derived proteotypic peptides to be used as drought tolerance markers in Quercus ilex

Project description:Drought is considered one of the main causes of mortality of holm oak (Quercus ilex) upon seedling plantations in reforestation programs. Although Q. ilex shows high adaptability to extreme climate conditions prevailing in Southern Spain, the genetic variability inherent to this species could be associated with a differential response depending on populations or individuals. The objective of this work was to identify proteins and derived proteotypic peptides to be used as markers of tolerance to drought in holm oak using a targeted post-acquisition proteomics approach. The study was based on a set of proteins identified by shotgun (LC-MSMS) from a drought experiment carried out in Q. ilex seedlings from four Andalusian provenances (Granada, Huelva, Cadiz and Seville). A double strategy, shotgun protein quantification and target peptides quantification post-acquisition data analysis based on proteotypic peptides, was used. For this purpose, an initial list of target peptides consisting in proteotypic peptides derived of proteins highly represented in drought conditions was compiled. Then, the proteotypic peptides list and the raw files from the shotgun experiment were imported into the Skyline software to quantify the relative abundance of the fragments ion peaks. Those peptides significantly more abundant in drought conditions at least in two populations were selected as putative markers of tolerance to drought. These corresponded to proteins belonged to redox, stress related proteins, synthesis, folding and degradation, and primary and secondary metabolism functional groups. Two proteins were found to be increased in three populations, making them especially interesting for validation in subsequent experiments as markers of drought tolerance.

2023-03-11 | PXD023782 | Pride

Proteomic response to drought and Phytophthora cinnamomi in Quercus ilex.

Project description:Biotic and abiotic stresses are predicted to be the main drivers of forest tree decline and mortality in a climatic change scenario. It occurs, for example, in Quercus ilex, the main component of the Mediterranean forest, becoming a major environmental, economic and social concern. The decline syndrome is the result of factors interrelated in time and space. Breeding, through variability and elite genotype selection, is the only plausible strategy for forest management and conservation in nondomesticated, orphan species as is the case of the genus Quercus. By using a shotgun proteomics approach, the effect and the responses to combined drought stress and pathogen (Phytophthora cinnamomi) have been analyzed in two Holm oak populations with contrasting responses to each individual stress. Proteomics data are correlated with that of plant survival, damage symptoms, leaf chemical composition and physiological phenotypes (water content and photosynthetic activity). Changes in the protein profile depended on the population, stress, and time, with some consistent upaccumulated proteins related to synthesis, primary and secondary metabolism, and cell wall are discussed.

2021-08-18 | PXD025704 | Pride

Quercus ilex

Project description:Quercus ilex overview

| PRJNA407388 | ENA

Quercus ilex

Project description:Quercus ilex transcriptome assembly

| PRJNA407283 | ENA

Quercus ilex

Project description:Quercus ilex Raw sequence reads

| PRJNA393086 | ENA

PacBio Iso-Seq transcriptome for California Valley Oak, Quercus lobata (SW786)

Project description:Iso-Seq "full length" transcript sequences were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

2021-05-22 | GSE174827 | GEO

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