We performed dual‑organism single‑nucleus RNA‑seq on Vitis vinifera leaves infected with the powdery mildew fungus Erysiphe necator at 1 and 5 days post‑infection, generating atlases of >100,000 grapevine nuclei and >3,000 pathogen nuclei. The study identified cell‑type‑specific markers, pathogen structures, and spatially distinct host defense programs, and used weighted gene co‑expression network analysis to reveal hubs linking pattern‑triggered and effector‑triggered immunity.

The study demonstrates that the IRE1/bZIP60 and bZIP17 arms of the unfolded protein response are conserved and transcriptionally active in Vitis vinifera under a range of abiotic stresses (heat, osmotic, copper) and biotic challenges (Plasmopara viticola, Botrytis cinerea). VvbZIP60 undergoes unconventional splicing following DTT or tunicamycin treatment, while VvbZIP17 is up‑regulated in green berries associated with basal resistance. Together, these findings reveal broad stress‑responsive regulation of grapevine UPR pathways.

The study presents a high-quality genome assembly for the nickel hyperaccumulator Noccaea caerulescens and uses it as a reference for comparative transcriptomic analyses across different N. caerulescens accessions and the non‑accumulating relative Microthlaspi perfoliatum. It identifies a limited set of metal transporters (NcHMA3, NcHMA4, NcIREG2, and NcIRT1) whose elevated expression correlates with hyperaccumulation, and demonstrates that frameshift mutations in NcIRT1 can abolish the trait, indicating an ancient, transporter‑driven origin of nickel hyperaccumulation.

The study identifies the transcription factor MdBRC1 as a key inhibitor of bud growth during the ecodormancy phase in apple (Malus domestica), directly regulating dormancy‑associated genes and interacting with the flowering promoter MdFT2 to modulate bud break. Comparative transcriptomic analysis and gain‑of‑function experiments in poplar demonstrate that MdFT2 physically binds MdBRC1, attenuating its repressive activity and acting as a molecular switch for the transition to active growth.

The study introduced full-length SOC1 genes from maize and soybean, and a partial SOC1 gene from blueberry, into tomato plants under constitutive promoters. While VcSOC1K and ZmSOC1 accelerated flowering, all three transgenes increased fruit number per plant mainly by promoting branching, and transcriptomic profiling revealed alterations in flowering, growth, and stress‑response pathways.

The study examined how varying levels of ammonium nitrate nutrition affect esca disease incidence, vine physiology, and leaf metabolite composition in Vitis vinifera cv. Sauvignon blanc. Nitrogen deficiency reduced disease occurrence and stem growth while enhancing phenylpropanoid production, whereas medium nutrition increased incidence and excess nitrogen had no clear effect. These results suggest that nitrogen-mediated changes in transpiration and secondary metabolism influence esca development, highlighting fertilization as a potential disease management tool.

The study establishes the dwarf grapevine cultivar Pixie as a model for smoke taint research by producing a phased telomere-to-telomere diploid genome using HiFi long‑read sequencing and generating a comprehensive RNA‑seq expression atlas. Controlled smoke‑exposure experiments identified twelve smoke‑inducible glycosyltransferase genes (VviSIUGTs) whose expression dynamics mirrored glycoside accumulation, and co‑expression network and promoter analyses linked them to stress‑responsive regulatory modules, offering targets for breeding smoke‑resilient vines.

The study examined how methyl jasmonate (MeJA) induces terpene biosynthesis in Vitis vinifera cv. Gamay Freaux berry cell suspensions, focusing on the transcription factor MYC2 and its interaction with MYB24. Using transcriptomics and DAP-seq, the authors identified high‑confidence MYC2 target genes, including jasmonate‑related genes and terpene synthases, and showed that MeJA, but not ABA, triggers accumulation of terpenoid compounds.