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 characterizes a radiation‑induced root‑suppressed (Rs) mutant in tomato that displays dwarfism and pleiotropic defects in leaves, flowers, and fruits. Metabolite profiling and rescue with H2S donors implicate disrupted sulfur metabolism, and whole‑genome sequencing identifies promoter mutations in two root‑meristem‑specific sulfotransferase genes as likely contributors to the root phenotype.

The study identifies members of the REMORIN protein family as inhibitors of plasma membrane H⁺‑ATPases, leading to extracellular pH alkalinization that modulates cell surface processes such as steroid hormone signaling and coordinates root developmental transitions in Arabidopsis thaliana. This inhibition represents an ancient mechanism predating root evolution, suggesting that extracellular pH patterning has shaped plant morphogenesis.

The study used paired whole‑genome bisulphite sequencing and RNA‑seq on wheat landraces to investigate how DNA methylation patterns change during drought stress, revealing antagonistic trends across cytosine contexts and a key demethylation role for ROS1a family members. Gene‑body methylation correlated positively with expression but negatively with stress‑responsive changes, while drought‑induced hyper‑methylation of specific transposable elements, especially the RLX_famc9 LTR retrotransposon, appears to modulate downstream gene regulation via siRNA precursors.

The study examines how ectopic accumulation of methionine in Arabidopsis thaliana leaves, driven by a deregulated AtCGS transgene under a seed‑specific promoter, reshapes metabolism, gene expression, and DNA methylation. High‑methionine lines exhibit increased amino acids and sugars, activation of stress‑hormone pathways, and reduced expression of DNA methyltransferases, while low‑methionine lines show heightened non‑CG methylation without major transcriptional changes. Integrated transcriptomic and methylomic analyses reveal a feedback loop linking sulfur‑carbon metabolism, stress adaptation, and epigenetic regulation.

The study integrated 16 Arabidopsis thaliana whole‑genome bisulfite sequencing datasets from 13 stress experiments using a unified bioinformatic pipeline to map common and stress‑specific DNA methylation changes. Differentially methylated regions varied by stress type and methylation context, with CG DMRs enriched in gene bodies and CHG/CHH DMRs in transposable elements, some of which overlapped loci prone to stable epimutations. Gene ontology and TE enrichment analyses highlighted shared stress pathways and suggest environmental stress can generate heritable epigenetic variation.

High-quality PacBio HiFi draft genome assemblies were generated for three Bouteloua species (B. curtipendula, B. gracilis, B. eriopoda) with >98.5% BUSCO completeness. Gene prediction with Helixer produced inflated gene counts likely reflecting polyploidy and fragmented predictions, and panEDTA identified 25–40% transposable-element content dominated by LTR retrotransposons. These assemblies provide foundational references for comparative genomics within PACMAD grasses.

The study adapted high‑throughput transposable‑element sequencing and introduced the deNOVOEnrich pipeline to map somatic TE insertions in Arabidopsis thaliana, uncovering ~200,000 new events across wild‑type and epigenetic mutant lines. Somatic integration is non‑random and TE‑specific, with families like ONSEN, EVADE, and AtCOPIA21 preferentially targeting chromosomal arms, genic regions, and chromatin marked by H2A.Z, H3K27me3, and H3K4me1, especially near environmentally‑responsive genes such as resistance loci and biosynthetic clusters.

The study profiled root transcriptomes of Arabidopsis wild type and etr1 gain-of-function (etr1-3) and loss-of-function (etr1-7) mutants under ethylene or ACC treatment, identifying 4,522 ethylene‑responsive transcripts, including 553 that depend on ETR1 activity. ETR1‑dependent genes encompassed ethylene biosynthesis enzymes (ACO2, ACO3) and transcription factors, whose expression was further examined in an ein3eil1 background, revealing that both ETR1 and EIN3/EIL1 pathways regulate parts of the network controlling root hair proliferation and lateral root formation.

The study shows that the SnRK1 catalytic subunit KIN10 directs tissue-specific growth‑defense programs in Arabidopsis thaliana by reshaping transcriptomes. kin10 knockout mutants exhibit altered root transcription, reduced root growth, and weakened defense against Pseudomonas syringae, whereas KIN10 overexpression activates shoot defense pathways, increasing ROS and salicylic acid signaling at the cost of growth.