Search bioRxiv⌕ Search

Biology subjects

Sonego, P.

Publications and source records attributed to Sonego, P..

2 recordsLinked to original sources
bioRxiv2025

Developing the Grapevine Hydric Stress Atlas: A Meta-Analysis Resource for Exploring transcriptome Responses to Drought

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 to these challenges. Understanding the molecular mechanisms underlying drought responses in grapevines is essential for developing innovative molecular breeding strategies aimed at enhancing drought tolerance, improving cultivar resilience, and promoting agricultural sustainability. In this context, transcriptomic meta-analyses have proven valuable for uncovering global regulatory trends, gene co-expression networks and conserved biological responses across diverse conditions. As part of this study, 1107 public transcriptomic datasets from Illumina (631 runs) and ABI SOLID (476 runs) platforms were searched, reclassified and reanalyzed in the latest T2T genome assembly, in order to construct condition, cultivar and tissue-specific gene expression atlases associated with drought stress in grapevine. To facilitate exploration of this data, a web-based application, the Hydric Stress Atlas App (https://plantaeviz.tomsbiolab.com/vitviz/hydric_atlas/), was developed, as part of the Vitis module within the PlantaeViz platform. Together with this tool, we generated a whole-genome co-expression network using the same datasets (https://plantaeviz.tomsbiolab.com/vitviz/networks/non_agg_gcns/T2T/hydric_stress_TI/). This water stress condition-dependent GCN allows to explore and visualize gene co-expression relationships related to stress and identify network hubs holding novel drought stress regulators. We manually curated experimental metadata, and enabled the classification of transcriptomic data by cultivar, tissue, and drought tolerance. Finally, candidate genes associated with drought tolerance were identified via network topology analysis. These genes can be further used as molecular markers, or characterized via gene editing or cisgenesis, providing insights into their molecular roles in drought tolerance. This resource contributes to a deeper understanding of grapevine drought responses, offering a pathway for sustainable viticulture and innovative biotechnological solutions to address climate-related challenges.

plant biology↗
bioRxiv2025

A Grapevine MYC2-MYB24 Regulatory Module Activates Terpenoid Biosynthesis Upon Methyl Jasmonate Elicitation

Terpenes contribute to the characteristic flavor and aroma of grapes and their derived products while serving protective roles in plants against radiation, oxidative stress, and biotic challenges. The phytohormone methyl jasmonate (MeJA) mediates many of these processes and enhances terpene content in grape berries, but its underlying regulatory mechanism remains unclear. To address this, we treated Vitis vinifera cv. Gamay Freaux berry cell suspensions with MeJA (100 M) and cyclodextrins (50 mM), generating transcriptomic data. Upregulated genes (URGs) were enriched in jasmonic acid biosynthesis and signaling pathways, and transcription factors (TF) that represent novel candidates modulating MeJA responses. Inspection of these TFs in terms of their co-expressed genes allowed us to focus on MYC2, the sole bHLH IIIe subgroup member in grapevine. Using DAP-seq, we identified MYC2-bound genes and integrated them with MeJA-URGs and MYC2 co-expressed genes (CEGs) to produce a high-confidence target list. These targets were bound via a conserved G-box motif and included jasmonate-related genes (e.g., LOX and JAZ) and TFs such as MYB24, previously found to interact with MYC2 to activate terpenoid biosynthesis genes. Consistently, MeJA treatment induced 15 terpene synthase genes (TPS), eleven of which were bound by MYB24, MYC2, or both. Terpenoid compounds associated with these induced TPSs accumulated both intra- and extracellularly following treatment with MeJA and cyclodextrins, but not with abscisic acid (ABA). Our findings suggest that MYC2 regulates the jasmonate pathway and cooperates with MYB24 to mediate MeJA-induced terpene biosynthesis, shedding light on mechanisms that may extend to flower and fruit development, where this MYB-bHLH complex is also expressed.

plant biology↗