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 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 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 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.

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 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 examined salt-induced alterations in root system architecture across a diverse panel of wild and cultivated tomato accessions, identifying tolerant varieties with distinct lateral root strategies. By combining Bulk Segregant Analysis of an F2 population with GWAS, the authors pinpointed 22 candidate genes, further narrowing to two key regulators through RNA‑Seq and functional assays involving ethylene and ROS profiling. These findings reveal genetic targets for improving salt resilience in tomato root development.