The study examined early metabolic responses to salt stress in a salt‑tolerant alfalfa cultivar, focusing on SnRK1 activity, sucrose, and trehalose‑6‑phosphate dynamics during leaf expansion. Hydroponically grown plants exposed to 200 mM NaCl showed rapid, wave‑like SnRK1 activation within 1 hour, a transient decline in chloroplast performance, and an uncoupling of the Tre6P‑sucrose regulatory link, with a second SnRK1 peak correlating with reduced leaf growth. Exogenous sucrose inhibited SnRK1 activity, highlighting early SnRK1 activation as a pivotal component of salt stress adaptation.

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.

The study shows that silencing of NOR2 rRNA genes in Arabidopsis thaliana depends primarily on CHH-context cytosine methylation, particularly mediated by CMT2 and the chromatin remodeler DDM1, rather than CG or CHG methylation. Comparative promoter analysis revealed a prevalence of CHH sites in plant rDNA promoters, explaining why CHH methylation mutants disrupt NOR2 silencing more strongly, while NOR2 loci are hyper‑methylated and more condensed than NOR4.