Proteomic and Metabolomic Analysis of the Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought.

Holm oak () is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish "dehesa", making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva.

A first draft genome of holm oak ( subsp. ), the most representative species of the Mediterranean forest and the Spanish agrosylvopastoral ecosystem "".

The holm oak ( subsp. ) is the most representative species of the Mediterranean Basin and the agrosylvopastoral Spanish "" ecosystem. Being part of our life, culture, and subsistence since ancient times, it has significant environmental and economic importance.

Multiomics Molecular Research into the Recalcitrant and Orphan Tree Species: Why, What for, and How.

The holm oak ( L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas.

Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species .

Proteases and protease inhibitors have been identified in the recalcitrant species using and wet methods, with focus on those present in seeds during germination. analyses showed that the transcriptome database contained 2,240 and 97 transcripts annotated as proteases and protease inhibitors, respectively. They belonged to the different families according to MEROPS, being the serine and metallo ones the most represented.

Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for .

Drought is one of the main causes of mortality in holm oak () seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a role in the differential response of some populations and individuals. The aim of this work was to identify proteins and derived proteotypic peptides potentially useful as putative markers for drought tolerance in holm oak by using a targeted post-acquisition proteomics approach.

Quercus ilex pollen allergen, Que i 1, responsible for pollen food allergy syndrome caused by fruits in Spanish allergic patients.

Background: Pollen food allergy syndrome (PFAS) related to PR10 from vegetables is common in northern Europe, whereas in Mediterranean countries PFAS has been preferentially associated with profilins. However, there are pollen-allergic patients reactive to Bet v 1 in birch-free regions. Since it cannot be the primary sensitizer, there has to be another culprit.

Specific Protein Database Creation from Transcriptomics Data in Nonmodel Species: Holm Oak (Quercus ilex L.).

Proteomics encompasses efforts to identify all the proteins of a proteome, with most of studies about plant proteomics based on a bottom-up mass spectrometry (MS) strategy, in which the proteins are subjected to digestion by trypsin and the tryptic fragments are subjected to MS analysis. The identification of proteins from MS/MS spectra has been performed using different algorithms (Mascot, Sequest) against plant protein sequence databases such as UniProtKB or NCBI_Viridiplantae. But these databases are not the best choice for nonmodel species where they are underrepresented, resulting in poor identification rates.

Protein Interaction Networks: Functional and Statistical Approaches.

The evolution of next-generation sequencing and high-throughput technologies has created new opportunities and challenges in data science. Currently, a classic proteomics analysis can be complemented by going a step beyond the individual analysis of the proteome by using integrative approaches. These integrations can be focused either on inferring relationships among proteins themselves, with other molecular levels, phenotype, or even environmental data, giving the researcher new tools to extract and determine the most relevant information in biological terms.

Proteomics, Holm Oak () and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as , , , and . This review assesses the potential and limitations of the proteomics approaches and is focused on as a model species and other forest tree species. Proteomics has been used with since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus or .

Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome.

Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak (Quercus ilex) transcriptome.

A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species .

Holm oak () is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral "dehesa" ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the knowledge on the chemical composition and metabolism of this tree species, the employment of a holistic and multi-omics approach, in the Systems Biology direction would be necessary.