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 investigates the evolutionary shift from archegonial to embryo‑sac reproduction by analyzing transcriptomes of Ginkgo reproductive organs and related species. It reveals that the angiosperm pollen‑tube guidance module MYB98‑CRP‑ECS is active in mature Ginkgo archegonia and that, while egg cell transcription is conserved, changes in the fate of other female gametophyte cells drove the transition, providing a molecular framework for this major reproductive evolution.

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.

A comparative physiological study of persimmon cultivars with flat (Hiratanenashi) and round (Koushimaru) fruit shapes revealed that differences in cell proliferation, cell shape, and size contribute to shape variation. Principal component analysis of elliptic Fourier descriptors tracked shape changes, while histology and transcriptome profiling identified candidate genes, including a WOX13 homeobox gene, potentially governing fruit shape development.

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.

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.

The study investigates the role of the Arabidopsis transcription factor AtMYB93 in sulfur (S) signaling and root development, revealing that AtMYB93 mutants exhibit altered expression of S transport and metabolism genes and increased shoot S levels, while tomato plants overexpressing SlMYB93 show reduced shoot S. Transcriptomic profiling, elemental analysis, and promoter activity assays indicate that AtMYB93 contributes to root responses to S deprivation, though functional redundancy masks clear phenotypic effects on lateral and adventitious root formation.