A5043123403- Horticultural and Viticultural Research
- Plant Gene Expression Analysis
- Fermentation and Sensory Analysis
- Plant biochemistry and biosynthesis
- Sirtuins and Resveratrol in Medicine
- Plant Pathogens and Fungal Diseases
- Biochemical and biochemical processes
- Antioxidant Activity and Oxidative Stress
- Gene expression and cancer classification
- Plant Reproductive Biology
- Mosquito-borne diseases and control
- Nuts composition and effects
- Plant Physiology and Cultivation Studies
- Autophagy in Disease and Therapy
- Wine Industry and Tourism
- Plant Molecular Biology Research
- Plant and Biological Electrophysiology Studies
- Insect symbiosis and bacterial influences
- Plant Stress Responses and Tolerance
- Enzyme-mediated dye degradation
- Endoplasmic Reticulum Stress and Disease
- Identification and Quantification in Food
- GABA and Rice Research
- Plant and Fungal Interactions Research
- Molecular Biology Techniques and Applications
Institute for Integrative Systems Biology
2021-2024
Universitat de València
2021-2024
Fondazione Edmund Mach
2024
Parc Científic de la Universitat de València
2022
The Pirbright Institute
2020
The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators this but extent control has not deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows genome-wide TF-binding site interrogation grape. We obtained 5190 and 4443 binding events assigned to 4041 3626 genes MYB14 MYB15, respectively (approximately 40% peaks located within −10 kb start...
The genome sequence of the diploid and highly homozygous Vitis vinifera genotype PN40024 serves as reference for many grapevine studies. Despite several improvements to assembly, its current version PN12X.v2 is quite fragmented only represents haploid state with mixed haplotypes. In fact, being nearly homozygous, this contains heterozygous regions that are yet be resolved. Taking opportunity long-read sequencing technologies offer fully discriminate haplotype sequences, an improved...
Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this specially challenging in grapevine, one oldest fruit crops grown worldwide, which known to have more than 30,000 Well-established research communities studying model organisms created maintained, public private funds, diverse range online tools databases serving as repositories genomes gene...
The abundance of transcriptomic data and the development causal inference methods have paved way for gene network analyses in grapevine. Vitis OneGenE is a mining tool that finds direct correlations between genes, thus producing association networks. As proof concept, stilbene synthase regulatory obtained with has been compared published co-expression analysis experimental data, including cistrome MYB stilbenoid regulators. case study, two secondary metabolism pathways stilbenoids lignin...
Tomato (Solanum lycopersicum) is a globally important crop, yet the gene regulatory networks (GRNs) controlling expression remain poorly understood. In this study, we constructed GRNs for roots, leaves, flowers, fruits, and seeds by inferring transcription factor (TF)–target interactions from over 10,000 RNA-seq libraries using GENIE3 algorithm. We refined these with co-expression data computational predictions of TF binding sites. Our confirmed key regulators, including TOMATO AGAMOUS LIKE...
Climate change poses a significant threat to agriculture, particularly in regions where increased drought periods, abnormal heat, and intensified pest pressure threaten crop productivity. Viticulture, as one of the most economically important crops, is highly vulnerable these challenges. Understanding molecular mechanisms underlying responses grapevines essential for developing innovative breeding strategies aimed at enhancing tolerance, improving cultivar resilience, promoting agricultural...
Humulus lupulus L. (hop) is a multipurpose crop valued for its essential role in beer production and bioactive compounds with recognized medicinal properties. Otherwise, climate change represents major challenge to agriculture, particularly impacting the cultivation of crops stenoecious characteristics, such as hop. This highlights urgent need enhance resilience adverse environmental conditions. The phytohormone abscisic acid (ABA) key regulator plant responses abiotic stress, yet ABA...
Aedes aegypti Act4 is a paralog of the Drosophila melanogaster indirect flight muscle actin gene Act88F . has been shown to be haploinsufficient for in both males and females (amorphic mutants are dominant). Whereas expressed muscles females, expression substantially female-specific. We therefore used CRISPR/Cas9 homology directed repair examine phenotype two Culicine mosquitoes, Culex quinquefasciatus A screen dominant female-flightless Cx identified one such mutant associated with six base...
Abstract Mulberry ( Morus alba L.) is considered a millenary medicinal plant and food source for silkworms. Different M. extracts offer variety of biological pharmacological properties that are in part attributed to stilbenoids, small group phenylpropanoids include resveratrol oxyresveratrol. These naturally present non-renewable parts mulberry trees, impeding their efficient extraction. As way bypass this spatiotemporal restriction, we generated cell suspensions from twigs demonstrated the...
Abstract Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets certain species represents an opportunity to explore underutilized network aggregation approaches. In fact, aggregated GCNs (aggGCNs) highlight robust interactions and improve functional connectivity. We applied evaluated two different methods on public grapevine RNA-Seq from three tissues (leaf, berry, ‘all organs’). Our results show...
ABSTRACT Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets these species represents an opportunity to explore underutilized network aggregation approaches that highlight robust interactions and improve functional connectivity. We applied evaluated two different methods on public grapevine RNA- Seq belonging three tissue conditions (leaf, berry ‘all organs’). Our results show co-occurrence-based...
Abstract The genome sequence assembly of the diploid and highly homozygous V. vinifera genotype PN40024 serves as reference for many grapevine studies. Despite several improvements assembly, its current version PN12X.v2 is quite fragmented only represents haploid state with mixed haplotypes. In fact, despite nearly homozygous, it still contains various heterozygous regions. Taking opportunity that long-read sequencing technologies offer to fully discriminate haplotype sequences considering...
Water tolerance in plants is often associated with the accumulation of osmotic protectants, which are secondary metabolites that can help plant to cope water stress. One key protectants a sugar called Raffinose, synthesized by family enzymes Raffinose synthases. In this work, we focused on one these enzymes, VviRAF2, gene shows different expression levels and genetic variants (SNPs) among grapevine cultivars, ranging from tolerant susceptible stress, transcription factors may regulate...
Throughout the growing season, grapevine frequently encounters environmental challenges associated with heat and light radiation stress, especially during ripening stage, thereby constraining yield quality of berries. MYB24 has been previously proposed to control responses late fruit stages, it found require co-factor MYC2. We have generated transcriptomic data from leaves transiently co-transformed Differential expression analysis revealed 179 up-regulated genes (URGs). Considering tissue...
Addressing the opportunities and challenges of genomics methods in grapevine (Vitis vinifera L.) requires development a comprehensive accurate reference genome annotation. We aimed to create new gene annotation for PN40024 by integrating highly complete T2T assembly manually curated PN40024.v4 Here, we present novel workflow enhance incorporating past community input found PN40024.v4. The pipeline's containerization will improve workflow's reproducibility flexibility, facilitating its...
Abstract Grapevine ( Vitis vinifera L.) is the world's third most valuable horticultural crop, and current environmental scenario massively shifting grape cultivation landscape. The increase in heatwaves drought episodes alter fruit ripening, compromise yield vine survival, intensifying pressure on using limited water resources. ABA a key phytohormone that reduces canopy transpiration helps plants to cope with deficit. However, exogenous application of impractical because it suffers fast...
Abstract The increasing availability of omic data from non-model plant species has created a need for centralized, user-friendly platforms that maximize the utility these datasets. Here, we introduce PlantæViz, web-based tool designed integration, visualization, and analysis multi-omic across wide range species. PlantæViz offers advanced functionalities including gene co-expression regulatory networks, expression atlases, cistrome visualization metabolomics-transcriptomics providing robust...
Abstract The stilbenoid pathway is responsible for the production of resveratrol and its derivatives in grapevine. A few transcription factors (TFs) have been previously identified as regulators this but extent control yet to be fully understood. Here we demonstrate how DNA affinity purification sequencing (DAP-Seq) allows genome-wide TF binding site interrogation a non-model species. We obtained 5,190 4,443 events assigned 4,041 3,626 genes MYB14 MYB15, respectively (around 40% peaks being...
The combined variation in gene expression and environmental conditions during flower development can result phenotypic differences shape, size, material composition. Biomechanical responses organs due to external stimuli be mechanically measured at various levels. Here, we investigate snapdragon (Antirrhinum litigiosum) response vibro-acoustic by an interdisciplinary model updating framework. In a climate-controlled setup, sweep signals artificial representative of plant pollinator species...