The study used comparative transcriptomics of dorsal and ventral petals across development, alongside expression profiling in floral symmetry mutants, to identify genes linked to dorsal (AmCYC-dependent) and ventral (AmDIV-dependent) identities in Antirrhinum majus. In situ hybridisation validated axis‑specific and boundary‑localized expression patterns, revealing that a conserved NGATHA‑LIKE1‑BRASSINAZOLE‑RESISTANT1‑miR164 module has been co‑opted to regulate AmDIV targets and shape the corolla. These findings delineate regulatory modules coordinating dorsoventral and proximal‑distal patterning in zygomorphic flowers.

The study sequenced genomes of ericoid mycorrhiza‑forming liverworts and experimentally reconstituted the symbiosis, revealing a nutrient‑regulated state that supports intracellular colonization. Comparative transcriptomics identified an ancestral gene module governing intracellular symbiosis, and functional validation in Marchantia paleacea through genetic manipulation, phylogenetics, and transactivation assays confirmed its essential role. The findings suggest plants have retained and independently recruited this ancestral module for diverse intracellular symbioses.

A large-scale proteomic study in Arabidopsis thaliana identified over 32,000 isoform-specific peptides, confirming that alternative splicing, particularly intron retention, produces translated protein isoforms. Integrated proteogenomic analysis, SUPPA classification, and AlphaFold modeling revealed structural impacts and a non-linear regulation of transcript and protein abundance, with mutant phenotypes linking splicing to growth, chlorophyll content, and anthocyanin accumulation.

The study profiled root transcriptomes of Arabidopsis wild type and etr1 gain-of-function (etr1-3) and loss-of-function (etr1-7) mutants under ethylene or ACC treatment, identifying 4,522 ethylene‑responsive transcripts, including 553 that depend on ETR1 activity. ETR1‑dependent genes encompassed ethylene biosynthesis enzymes (ACO2, ACO3) and transcription factors, whose expression was further examined in an ein3eil1 background, revealing that both ETR1 and EIN3/EIL1 pathways regulate parts of the network controlling root hair proliferation and lateral root formation.

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 phospho‑proteomics to uncover rapid phosphorylation changes in Arabidopsis seedlings upon light or sucrose exposure, identifying RS41 as a hyperphosphorylated SR protein. By creating single and higher‑order mutants of four RS genes, the authors demonstrated that these RS proteins are essential for photomorphogenic development and regulate light‑dependent alternative splicing, with loss of all four causing sterility.

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 investigated how Arabidopsis thaliana SR protein kinases (AtSRPKs) regulate alternative RNA splicing by using chemical inhibitors of SRPK activity. Inhibition with SPHINX31 and SRPIN340 caused reduced root growth and loss of root hairs, accompanied by widespread changes in splicing and phosphorylation of genes linked to root development and other cellular processes. Multi‑omics analysis (transcriptomics and phosphoproteomics) revealed that AtSRPKs modulate diverse splicing factors and affect the splicing landscape of numerous pathways.