The study used transcriptomic profiling to compare tomato (Solanum lycopersicum) responses to three evolutionarily distant pathogens—nematodes, aphids, and oomycetes—during compatible interactions, identifying differentially expressed genes and key host hubs. Integrating public datasets and performing co‑expression and GO enrichment analyses, the authors mapped shared dysregulation clusters and employed Arabidopsis interactome data to place tomato candidates within broader networks, highlighting potential targets for multi‑pathogen resistance.

The authors compiled and standardized published data on Rubisco dark inhibition for 157 flowering plant species, categorizing them into four inhibition levels and analyzing phylogenetic trends. Their meta‑analysis reveals a complex, uneven distribution of inhibition across taxa, suggesting underlying chloroplast microenvironment drivers and providing a new resource for future photosynthesis improvement efforts.

The study investigates the role of the chromatin regulator MpSWI3, a core subunit of the SWI/SNF complex, in the liverwort Marchantia polymorpha. A promoter mutation disrupts male gametangiophore development and spermiogenesis, causing enhanced vegetative propagation, and transcriptomic analysis reveals that MpSWI3 regulates genes controlling reproductive initiation, sperm function, and asexual reproduction, highlighting its ancient epigenetic role in balancing vegetative and reproductive phases.

The study performed comparative gene expression profiling across four rice accessions—from shoot apical meristem to primordia stage P5—to delineate developmental and photosynthetic transitions in leaf development. By integrating differential expression and gene regulatory network analyses, the authors identified stage-specific regulatory events and key transcription factors, such as RDD1, ARID2, and ERF3, especially in the wild rice Oryza australiensis, offering a comprehensive framework for optimizing leaf function.

Foliar application of Trichoderma harzianum cell‑free culture filtrates (CF) increased fruit yield, root growth, and photosynthesis in a commercial tomato cultivar under prolonged water deficit in a Mediterranean greenhouse. Integrated physiological, metabolite, and transcriptomic analyses revealed that CF mitigated drought‑induced changes, suppressing about half of water‑stress responsive genes, thereby reducing the plant’s transcriptional sensitivity to water scarcity.

The study functionally characterizes three tomato CNR/FWL proteins (SlFWL2, SlFWL4, SlFWL5) and demonstrates that SlFWL5 localizes to plasmodesmata, where it regulates leaf size and morphology by promoting cell expansion likely through cell‑to‑cell communication. Gain‑ and loss‑of‑function transgenic tomato lines reveal that SlFWL5 is a key regulator of organ growth via modulation of plasmodesmatal signaling.

The study constructs a ~1‑million‑cell single‑nuclei transcriptome atlas of Arabidopsis leaves to reveal that drought stress accelerates transcriptional programs associated with maturation and aging, thereby limiting leaf growth in proportion to stress intensity. Targeted upregulation of FERRIC REDUCTION OXIDASE 6 in mesophyll cells partially rescues leaf growth under drought, demonstrating the functional relevance of these transcriptional changes.

The study examined transcriptomic responses of the tropical seagrass Halophila stipulacea from a pristine and an impacted site under single and combined thermal and excess nutrient stress in mesocosms. Combined stress caused greater gene reprogramming than individual stresses, with thermal effects dominating and the impacted population showing reduced plasticity but higher resilience. Core stress‑response genes were identified as potential early field indicators of environmental stress.