The study compares transcriptional, proteomic, and metabolomic responses of wild‑type Arabidopsis and a cyp71A27 mutant to a plant‑growth‑promoting Pseudomonas fluorescens strain and a pathogenic Burkholderia glumeae strain, revealing distinct reprogramming and an unexpected signaling role for the non‑canonical P450 CYP71A27. Mutant analysis showed that loss of CYP71A27 alters gene and protein regulation, especially during interaction with the PGP bacterium, while having limited impact on root metabolites and exudates.

The study presents a chromosome-level reference genome for the invasive fern Lygodium microphyllum and compares the transcriptomic and epigenomic profiles of its haploid gametophyte and diploid sporophyte phases, revealing differential regulation of developmental genes and similar methylation patterns across tissues. Base‑pair resolution methylome data and freezing‑stress experiments show that each life phase employs distinct molecular pathways for stress response, emphasizing the importance of considering both phases in invasive‑species management.

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 investigates how miR394 influences flowering time in Arabidopsis thaliana by combining transcriptomic profiling of mir394a mir394b double mutants with histological analysis of reporter lines. Bioinformatic analysis identified a novel lncRNA overlapping MIR394B (named MIRAST), and differential promoter activity of MIR394A and MIR394B suggests miR394 fine‑tunes flower development through transcription factor and chromatin remodeler regulation.

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.

The study examined transposable element (TE) silencing in the duckweed Spirodela polyrhiza, which exhibits unusually low DNA methylation, scarce 24‑nt siRNAs, and missing RdDM components. While degenerated TEs lack DNA methylation and H3K9me2, they retain heterochromatin marks H3K9me1 and H3K27me1, whereas the few intact TEs show high DNA methylation and H3K9me2, indicating a shift in RdDM focus toward potentially active TEs and suggesting heterochromatin can be maintained independently of DNA methylation in flowering plants.