The authors created a high‑throughput yeast two‑hybrid platform using Arabidopsis F‑box and U‑box E3 decoys to map E3‑substrate interactions, screening 283 E3 variants against 21 core circadian clock regulators and identifying 77 candidate pairs. They validated that PUB18 interacts with LHY and JMJD5, promotes their ubiquitination in planta, and that PUB18 and its homolog PUB19 redundantly regulate the circadian clock, demonstrating the utility of the decoy system for dissecting ubiquitination networks.

The study reveals that early PAMP-triggered immune responses, such as flg22‑induced FRK1 transcription and ROS production, are heightened at subjective dusk compared to dawn in Arabidopsis. Overexpression of the clock gene TOC1 dampens these defenses and increases susceptibility to Pseudomonas syringae, while flg22 and elf18 treatments reset the rhythmic expression of core clock genes CCA1 and TOC1.

The study presents the first single‑nucleus transcriptome atlas for the CAM plant Mesembryanthemum crystallinum, revealing cell‑type specific transcriptional changes during the C3‑to‑CAM transition. Integrating snRNA‑seq with a 24‑hour bulk RNA‑seq time course identified PPCK1 within a circadian‑enriched co‑expression network, and functional assays showed that the ice‑plant HY5 directly activates PPCK1, a regulatory relationship absent in Arabidopsis thaliana. These findings highlight a rewiring of transcriptional regulation underlying CAM evolution and provide a target for engineering drought‑resilient crops.

The study used comparative transcriptomics across Erysimum species to identify two 2‑oxoglutarate‑dependent dioxygenases, CARD5 and CARD6, responsible for the 14β‑ and 21‑hydroxylation steps in cardenolide biosynthesis in Erysimum cheiranthoides. Knockout mutants lacking these genes accumulated pathway intermediates, and transient expression in Nicotiana benthamiana confirmed their enzymatic functions, while structural modeling pinpointed residues linked to neofunctionalization.

The study used comparative and de‑novo transcriptomic analyses in poplar to uncover plant and fungal gene regulons that govern ectomycorrhizal (ECM) compatibility, distinguishing general fungal‑sensing responses from ECM‑specific pathways. Key findings include modulation of jasmonic acid‑related defenses, coordinated regulation of secretory and cell‑wall remodeling genes, and dynamic expression of the Common Symbiosis Pathway during early and mature symbiosis stages.

The study compared early protective, repair, and stress responses to chronic gamma irradiation in the radiosensitive conifer Norway spruce (Picea abies) and the radiotolerant Arabidopsis thaliana. Norway spruce exhibited growth inhibition, mitochondrial damage, and higher DNA damage at low dose rates, while Arabidopsis maintained growth, showed minimal organelle damage, and activated DNA repair and antioxidant genes even at the lowest dose rates. Transcriptomic analysis revealed that the tolerant species mounts a robust transcriptional response at low doses, whereas the sensitive species only responds at much higher doses.

The study used comparative transcriptomics to examine how Fusarium oxysporum isolates with different lifestyles on angiosperms regulate effector genes during infection of the non‑vascular liverwort Marchantia polymorpha. Core effector genes on fast core chromosomes are actively expressed in the bryophyte host, while lineage‑specific effectors linked to angiosperm pathogenicity are silent, and disruption of a compatibility‑associated core effector alters the expression of other core effectors, highlighting conserved fungal gene networks across plant lineages.

The study demonstrates that phosphorylation of the core circadian repressor TOC1, especially at serine 175, is essential for its interaction with FHY3 and PIF5 at the CCA1 promoter, thereby modulating CCA1 repression. While TOC1 phosphorylation is required for CCA1 regulation, LHY expression depends on TOC1 but not on its phosphostate, indicating distinct repression mechanisms. Genome-wide analyses reveal that TOC1’s phosphostate enhances chromatin association and robust rhythmic transcription.

The study demonstrates that dihydroxy B‑ring flavonoids modulate the amplitude of the core circadian clock gene reporter TOC1:LUC in Arabidopsis by affecting cellular H2O2 levels, rather than auxin transport. Reducing reactive oxygen species restored normal TOC1:LUC amplitude in flavonoid‑deficient seedlings, and altered chloroplast Ca2+ levels suggest a retrograde signaling component.

The study generated a high-quality genome assembly for Victoria cruziana and used comparative transcriptomics to identify anthocyanin biosynthesis genes and their transcriptional regulators that are differentially expressed between white and light pinkish flower stages. Differential expression of structural genes (VcrF3H, VcrF35H, VcrDFR, VcrANS, VcrarGST) and transcription factors (VcrMYB123, VcrMYB-SG6_a, VcrMYB-SG6_b, VcrTT8, VcrTTG1) correlates with the observed flower color change.