Phosphite (Phi) and phosphate (Pi) share the same root uptake system, but Phi acts as a biostimulant that modulates plant growth and disease resistance in a species‑ and Pi‑dependent manner. In Arabidopsis, Phi induces hypersensitive‑like cell death and enhances resistance to Plectosphaerella cucumerina, while in rice it counteracts Pi‑induced susceptibility to Magnaporthe oryzae and Fusarium fujikuroi, accompanied by extensive transcriptional reprogramming.

The study investigates the gene regulatory network (GRN) controlling flowering time in the allotetraploid crop Brassica napus by comparing its transcriptome to that of Arabidopsis thaliana. While most orthologous gene pairs show conserved expression dynamics, several flowering‑time genes display regulatory divergence, especially under cold conditions, indicating subfunctionalisation among paralogues. Despite these differences, the overall GRN topology remains similar to Arabidopsis, likely due to retention of multiple paralogues.

The study generated a dataset of 420 sgRNAs targeting promoters, exons, and introns of 137 tomato genes in protoplasts, linking editing efficiency to chromatin accessibility, genomic context, and sequence features. Open chromatin sites showed higher editing rates, while transcriptional activity had little effect, and a subset of guides produced near‑complete editing with microhomology‑mediated deletions. Human‑trained prediction models performed poorly, highlighting the need for plant‑specific guide design tools.

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.

The study investigates the role of the chromatin regulator MpSWI3, a core subunit of the SWI/SNF complex, in the liverwort Marchantia polymorpha. A promoter mutation disrupts male gametangiophore development and spermiogenesis, causing enhanced vegetative propagation, and transcriptomic analysis reveals that MpSWI3 regulates genes controlling reproductive initiation, sperm function, and asexual reproduction, highlighting its ancient epigenetic role in balancing vegetative and reproductive phases.

The study integrates genome, transcriptome, and chromatin accessibility data from 380 soybean accessions to dissect the genetic and regulatory basis of symbiotic nitrogen fixation (SNF). Using GWAS, TWAS, eQTL mapping, and ATAC-seq, the authors identify key loci, co‑expression modules, and regulatory elements, and validate the circadian clock gene GmLHY1b as a negative regulator of nodulation via CRISPR and CUT&Tag. These resources illuminate SNF networks and provide a foundation for soybean improvement.

The study examines how the SnRK1 catalytic subunit KIN10 integrates carbon availability with root growth regulation in Arabidopsis thaliana. Loss of KIN10 reduces glucose‑induced inhibition of root elongation and triggers widespread transcriptional reprogramming of metabolic and hormonal pathways, notably affecting auxin and jasmonate signaling under sucrose supplementation. These findings highlight KIN10 as a central hub linking energy status to developmental and environmental cues in roots.

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.