The study examined DNA methylation dynamics in Arabidopsis thaliana shoots and roots under heat, phosphate deficiency, and combined stress using whole-genome bisulfite sequencing, small RNA‑seq, and RNA‑seq. Distinct stress‑specific methylation patterns were identified, with heat and combined stress causing CHH hypomethylation, phosphate deficiency causing hyper‑ and hypomethylation in shoots and roots respectively, and the combined stress exhibiting a unique signature independent of additive effects. Methylation changes were concentrated in transposable elements and regulatory regions, implicating RdDM and CMT2 pathways and suggesting a role in chromatin accessibility rather than direct transcriptional control.

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 mapped the cis‑regulatory landscape of the winter rapeseed cultivar Express617, identifying thousands of novel regulatory elements and characterizing super‑enhancers that are asymmetrically enriched in the Cn subgenome of Brassica napus. An in‑silico pipeline combining population‑level expression data and machine‑learning models revealed that many SE‑associated genes are expressed above predicted levels, and structural variants disrupting SEs lead to reduced gene expression, highlighting their functional importance for gene regulation and breeding.

The study investigates the wheat Pm3 NLR allelic series, revealing that near-identical Pm3d and Pm3e alleles confer broad-spectrum resistance by recognizing multiple, structurally diverse powdery mildew effectors. Using chimeric NLR constructs, the authors pinpoint specificity-determining polymorphisms and demonstrate that engineered combinations of Pm3d and Pm3e further expand effector recognition, showcasing the potential for durable wheat protection through NLR engineering.

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.

The study examined short‑term and transannual drought memory in cambium tissues of two Populus genotypes and four epitypes with modified DNA‑methylation machinery, revealing persistent hormone, transcript, and methylation changes one week after stress relief. Trees previously stressed in Year 1 displayed distinct physiological and molecular responses to a second drought in Year 2, indicating long‑term memory linked to stable CG‑context DNA methylation, with genotype‑dependent differences in plasticity and stability. These findings position the cambium as a reservoir for epigenetic stress memory and suggest exploitable epigenetic variation for tree breeding under drought.

The researchers created tomato lines overexpressing the autophagy gene SlATG8f and evaluated their performance under high-temperature stress. qRT‑PCR and physiological measurements revealed that SlATG8f overexpression enhances expression of autophagy‑related and heat‑shock protein genes, accelerates fruit ripening, and improves fruit quality under heat stress.

The study identifies an autophagy pathway that degrades plasma membrane-derived clathrin-coated vesicles (CCVs) during hyperosmotic stress, helping maintain membrane tension as cell volume decreases. Using live imaging and correlative microscopy, the authors show that the TPLATE complex subunits AtEH1/Pan1 and AtEH2/Pan1 act as selective autophagy receptors by directly binding ATG8, thereby removing excess membrane under drought or salt conditions.

Regenerative agriculture using a grass-clover ley increased wheat yields and macroaggregate stability despite reduced root biomass, but did not enhance soil carbon sequestration as measured by 14C retention. Drought further decreased photosynthate allocation to roots, especially in ley soils, while genotype effects on yield were minimal.

Using genome‑wide association studies in Arabidopsis thaliana, the authors identified the chromatin‑associated protein CDCA7 as a trans‑regulator that specifically controls CG methylation (mCG) and TE silencing. CDCA7 and its paralog CDCA7β bind the remodeler DDM1, modulating its activity without broadly affecting non‑CG methylation or histone variant deposition, and natural variation in CDCA7 regulatory sequences correlates with local ecological adaptation.