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Climate change and enhanced pollution levels are subjecting plants and crops to an increased number of different stressors, simultaneously or sequentially, generating conditions of multifactorial stress combination (MFSC). Although MFSC was shown to severely diminish plant growth, yield, and survival, how plants acclimate to increased levels of stress complexity is largely unknown. Here, we reveal that theArabidopsis thalianatranscriptional regulator basic helix-loop-helix 35 (bHLH35) is required for plant acclimation to a specific set of MFSC conditions that includes a combination of salinity, excess light, and heat, occurring simultaneously (but not to each of these stresses applied individually or in any other combination). Under the three-stress combination, bHLH35 interacts with no apical meristem/transcription activator factor/cup-shaped cotyledon 69 (NAC069), binds the promoter oflateral organ boundaries domain 31 (LBD31), and regulates the expression of transcripts involved in flavonoid metabolism and ethylene signaling. Our findings uncover a high degree of specificity in plant responses to stress combination, suggesting that different conditions of MFSC could require the function of specific genetic programs for acclimation. 

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied. 

Climate change is altering our environment, subjecting multiple agroecosystems worldwide to an increased frequency and intensity of abiotic stress conditions such as heat, drought, flooding, salinity, cold and/or their potential combinations. These stresses impact plant growth, yield and survival, causing losses of billions of dollars to agricultural productivity, and in extreme cases they lead to famine, migration and even wars. As the rate of change in our environment has dramatically accelerated in recent years, more research is urgently needed to discover and develop new ways and tools to increase the resilience of crops to different stress conditions. In this theme issue, new studies addressing the molecular, metabolic, and physiological responses of crops and other plants to abiotic stress challenges are discussed, as well as the potential to exploit these mechanisms in biotechnological applications aimed at preserving and/or increasing crop yield under our changing climate conditions. This article is part of the theme issue ‘Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the ‘Resilience Revolution’?’ 

Nitric oxide (NO) is a key regulator of plant development, growth, and responses to the environment. Together with hydrogen peroxide (H₂O₂), NO modifies the structure and function of proteins, controlling redox signaling. Although NO has been studied extensively at the cellular and subcellular levels, very little is known about changes in NO content at the whole‐plant level.Here, we report on the development of an aboveground whole‐plant live imaging method for NO. Using mutants with altered NO levels, as well as an NO donor/scavenger, we demonstrate the specificity of the detection method for NO.Arabidopsis thalianaplants were found to produce a basal level of NO under control conditions. NO levels accumulated enzymatically in plants following heat stress applied to the entire plant, as well as in a systemic manner following different locally applied stimuli. Similar or opposing accumulation patterns were also found for NO and H₂O₂during the response of plants to different stimuli.Our findings reveal that NO accumulates during the systemic response of plants to a local stimulus. In addition, they shed new light on the intricate relationships between NO and H₂O₂. The new method reported opens the way for multiple future studies of NO's role in plant biology. 

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend. 

Two plants connected via a Cuscuta bridge exchange rapid systemic calcium, electric, and reactive oxygen species signals, suggesting that Cuscuta may have beneficial effects to host plants.