The study examined how DNA methylation influences cold stress priming in Arabidopsis thaliana, revealing that primed plants exhibit distinct gene expression and methylation patterns compared to non-primed plants. DNA methylation mutants, especially met1 lacking CG methylation, showed altered cold memory and misregulation of the CBF gene cluster, indicating that methylation ensures transcriptional precision during stress recall.

The authors used a bottom‑up thermodynamic modelling framework to investigate how plants decode calcium signals, starting from Ca2+ binding to EF‑hand proteins and extending to higher‑order decoding modules. They identified six universal Ca2+-decoding modules that can explain variations in calcium sensitivity among kinases and provide a theoretical basis for interpreting calcium signal amplitude and frequency in plant cells.

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 identified and characterized 13 PIN-FORMED auxin transporter genes in the C4 monocot model Setaria viridis, revealing duplication events, unique structural features, and tissue‑specific expression patterns across developmental stages. Hormonal treatments in callus cultures demonstrated auxin‑responsive upregulation of several SvPIN genes, providing a foundation for future functional analyses and potential crop‑improvement strategies.

The study identifies three dihydroflavonol-4-reductase (DFR) gene copies in Fagopyrum, with the conserved DFR1 broadly expressed and the duplicated DFR2a and DFR2b harboring mutations in the substrate‑binding region, altered promoter motifs, and seed/ root‑specific expression. Comparative genomics, synteny, expression, promoter and selective pressure analyses support a DNA duplication‑inversion mechanism and early functional differentiation of the DFR2 copies.

The study uncovers the molecular evolution of Bowman‑Birk inhibitors (BBIs) in legumes and cereals, revealing two divergent gene families with seed‑specific and stress‑responsive subfamilies, and demonstrates that CRISPR/Cas9 knockout of seed‑specific BBIs in soybean markedly reduces trypsin and chymotrypsin inhibitor activities without affecting key agronomic traits. These findings highlight BBIs’ role in stress adaptation rather than core development and suggest a strategy for improving seed nutritional quality.

The study reveals that a conserved clade of pentatricopeptide repeat (PPR) genes in Arabidopsis thaliana generates secondary siRNAs that contribute to plant immunity, with these PPR loci undergoing extensive duplication and diversification to create a varied siRNA pool for pathogen defense. This PPR‑siRNA system is proposed as a novel family of defense genes with potential for engineering broad‑spectrum disease resistance.

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.

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 performed a comprehensive computational analysis of the Arabidopsis thaliana proteome, classifying 48,359 proteins by melting temperature (Tm) and melting temperature index (TI) and linking thermal stability to amino acid composition, molecular mass, and codon usage. Machine‑learning and evolutionary analyses revealed that higher molecular mass and specific codon pairs correlate with higher Tm, and that gene duplication has driven the evolution of high‑Tm proteins, suggesting a genomic basis for stress resilience.