The study generated the first single‑nucleus RNA‑sequencing dataset of tomato (Solanum lycopersicum) roots colonized by the arbuscular mycorrhizal fungus Rhizophagus irregularis, revealing distinct transcriptional programs in epidermal and cortical cells across stages of arbuscule development. Using unsupervised subclustering and a Motif‑Informed Network Inference (MINI‑EX) approach, the authors identified candidate transcription factors that may coordinate cell‑cycle reactivation and nutrient integration during symbiosis, offering a resource for future functional genetics.

The study assessed three savory essential oil–based formulations for controlling early blight caused by Alternaria solani in tomato, finding that formulation CC2020 most effectively reduced disease severity in both in vitro and greenhouse trials. CC2020 also helped maintain tomato fruit vitamin C levels and lowered fungal melanin production, indicating dual benefits for disease suppression and fruit quality.

The authors used a bottom‑up thermodynamic modelling framework to investigate how plants decode calcium signals, starting from Ca2+ binding to EF‑hand proteins and extending to higher‑order decoding modules. They identified six universal Ca2+-decoding modules that can explain variations in calcium sensitivity among kinases and provide a theoretical basis for interpreting calcium signal amplitude and frequency in plant cells.

The authors generated a high‑resolution 1.45‑billion‑contact Micro‑C map for cultivated tomato (Solanum lycopersicum), identifying ~4,600 long‑range chromatin loops that fall into promoter‑centered and Polycomb/heterochromatin‑associated classes. Comparative Micro‑C in wild tomatoes showed conserved loop anchors despite sequence turnover, and integration with transcriptomics revealed that promoter‑anchored loops can either activate or repress gene expression depending on the chromatin state of distal anchors.

The study conducted a genome-wide characterization of 247 lectin genes in tomato, revealing diverse domain architectures and evolutionary patterns shaped by whole-genome and small-scale duplications. Functional assays using virus-induced gene silencing demonstrated that two GNA-type chimerolectins act as negative regulators of immunity, with silencing enhancing resistance to Ralstonia solanacearum. These results underscore the structural innovation and immune-regulatory roles of lectin genes, offering targets for disease‑resistant tomato breeding.

The study examined how increasing copper concentrations affect root tip cells of Solanum lycopersicum, revealing that mitochondria are the first organelles to exhibit fragmentation, depolarization, and ROS accumulation, which trigger stress signaling cascades. Copper exposure also caused pronounced nuclear alterations, including chromatin condensation marked by reduced H3K4me3, nuclear shrinkage, and eventual cell death, highlighting chromatin remodeling as a key indicator of copper toxicity.

Using transparent root apex cells of Solanum lycopersicum, the study employed live‑cell fluorescence imaging, immunostaining, and super‑resolution microscopy to map the sequential collapse of organelles under lidocaine anesthesia. It reveals that mitochondria, lysosomes, vesicle trafficking, and especially the nucleus undergo time‑dependent damage, with reversible effects up to four hours but irreversible nuclear degradation and programmed cell death beyond that, highlighting potential protective strategies.

The study introduces a minimal precursor platform for synthetic trans-acting siRNAs (syn-tasiRNAs) in tomato, leveraging the endogenous SlmiR482b microRNA to produce functional silencing agents in both transgenic and virus-induced gene silencing (VIGS) systems. Minimal precursors successfully silenced endogenous genes and conferred resistance to tomato spotted wilt virus, and a transgene‑free delivery via crude extracts was demonstrated, highlighting a versatile tool for precision RNAi in Solanum lycopersicum.

The study generated and physiologically characterized tomato ELIP mutants (slelip) under various light conditions, finding no impairment in photosynthetic performance or increased photoinhibition. Using a pSlELIP1::Venus reporter, ELIP expression was localized primarily to epidermal guard cells rather than mesophyll, and mutants showed reduced stomatal conductance during dark‑to‑light transition, suggesting a role for ELIPs in guard‑cell light responses.

The authors engineered a double fluorescent reporter line in the tomato cultivar Micro‑Tom, using mTurquoise and mScarlet‑I driven by generative‑cell‑ and sperm‑cell‑specific promoters, respectively. They established a protocol that releases male gametes from pollen, stains them with SYTOX Red, and isolates viable generative cells, sperm cells, and vegetative nuclei via fluorescence‑activated cell sorting (FACS). This tool enables high‑purity, high‑quantity isolation of tomato male gametes for downstream omics studies.