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.

The study demonstrates that the chromatin remodeler DDM1 is essential for biomass heterosis in Arabidopsis thaliana hybrids, as loss of DDM1 function leads to reduced rosette growth and extensive genotype‑specific transcriptomic and DNA methylation changes. Whole‑genome bisulfite sequencing revealed widespread hypomethylation in ddm1 mutants, while salicylic acid levels were found unrelated to heterosis, indicating that epigenetic divergence, rather than SA signaling, underpins hybrid vigor.

The study examined molecular responses in grapevine leaves with and without esca symptoms, using metabolite profiling, RNA‑seq and whole‑genome bisulfite sequencing. Metabolic and transcriptomic changes were confined to symptomatic leaves and linked to local DNA‑methylation alterations, while asymptomatic leaves showed distinct but overlapping methylation patterns, some present before symptoms, indicating potential epigenetic biomarkers for early disease detection.

The study identifies GyrB3 as a novel nuclear factor that interacts with histone deacetylases to regulate transposable element silencing in plants, acting as a suppressor of IBM1 deficiency–induced epigenetic defects. Loss of GyrB3 reduces DNA methylation and increases H3 acetylation at TEs, demonstrating the importance of histone deacetylation for genome stability.

The study combined ecometabolomics of root exudates with fungal community profiling to assess how abiotic (soil moisture, temperature legacy) and biotic (microbial inoculum, plant density) treatments shape metabolite diversity and fungal assemblages in Guarea guidonia seedlings. While soil microbial legacy and moisture drove metabolite diversity, antimicrobial treatments altered metabolite composition, and fungal community structure was linked to metabolite profiles, revealing metabolite‑fungal associations as early indicators of plant response to disturbance.

The study examined gene expression, DNA methylation, and small RNA profiles in a Citrus hybrid (C. reticulata × C. australasica) using haplotype‑resolved subgenome assemblies, revealing allele‑specific expression and asymmetric CHH methylation that correlated with increased transcription and 24‑nt siRNA accumulation at promoters. This unconventional association suggests RNA‑directed DNA methylation (RdDM) can activate transcription in citrus fruit and provides a pipeline for epigenomic analysis of complex hybrids relevant to disease resistance breeding.

The study combined long‑read whole‑genome assembly, multi‑omics profiling (DNA methylation, mRNA, ribosome‑associated transcripts, tRNA abundance, and protein levels) in two Arabidopsis thaliana accessions to evaluate how genomic information propagates through the Central Dogma. Codon usage in gene sequences emerged as the strongest predictor of both mRNA and protein abundance, while methylation, tRNA levels, and ribosome‑associated transcripts contributed little additional information under stable conditions.

The study investigated how plant roots promote water infiltration through dry soil layers using dye tracing in model soil microcosms. Results indicate that dissolved root exudates, possibly by altering surface tension, are the primary drivers of infiltration, with root architecture also contributing. These insights suggest that root traits influencing exudation and structure could improve drought resistance in crops.

The study examined how altering ethylene biosynthesis (ACO1) or perception (etr1.1) in a hybrid poplar (P. tremula × P. tremuloides T89) influences the assembly of root and shoot fungal and bacterial communities, using amplicon sequencing and confocal microscopy. Ethylene modulation had limited impact on the sterile plant metabolome but triggered distinct primary and secondary metabolic changes in microbe‑colonized plants, correlating with reduced fungal colonisation of shoots and increased root fungal colonisation, while arbuscular mycorrhizal fungi and bacterial communities were largely unchanged.

Reduced activity of methylthioadenosine (MTA) nucleosidase causes MTA over‑accumulation in reproductive tissues, leading to lowered cysteine, methionine, and S‑adenosylmethionine levels and altered sulfur and energy metabolism. These metabolic disturbances trigger misregulation of cell‑cycle progression, widespread down‑regulation of developmental genes, and genome‑wide changes in DNA methylation patterns, highlighting the extensive role of MTA recycling in plant growth and methyl‑index maintenance.