The study applied the STOmics spatial transcriptomics platform to map gene expression at subcellular resolution in developing wheat (Triticum aestivum) seeds during grain filling, analyzing over four million transcripts. Eight functional cellular groups were identified, including four distinct endosperm clusters with radial expression patterns and novel marker genes, and subgenome‑biased expression was observed among specific paralogs. These results highlight spatial transcriptomics as a powerful tool for uncovering tissue‑specific and polyploid‑specific gene regulation in seeds.

The study combined spatial transcriptomics and single-nuclei RNA sequencing to map soybean (Glycine max) responses to Asian soybean rust caused by Phakopsora pachyrhizi, revealing two distinct host cell states: pathogen‑occupied regions and adjacent non‑infected regions that show heightened defense gene expression. Gene co‑expression network analysis identified a key immune‑related module active in the stressed cells, highlighting a cell‑non‑autonomous defense mechanism.

The study presents a multiplexed technique that applies both single‑cell RNA sequencing (scRNA‑seq) and single‑cell mass spectrometry metabolomics (scMS) to the same plant cell, enabling direct, cell‑by‑cell correlation of gene expression with metabolite levels. This integrated approach uncovers qualitative and quantitative relationships between biosynthetic gene activity and metabolite accumulation, advancing understanding of complex plant natural product pathways.

The study generated high-resolution single-cell and single-nucleus RNA‑seq transcriptome atlases for two independently evolved C4 dicots, Gynandropsis gynandra (NAD-ME) and Flaveria bidentis (NADP-ME), enabling detailed comparison of leaf cell types. Bundle sheath cells in both species displayed a gene‑expression profile resembling C3 mesophyll cells and shared a conserved set of C2H2 and DOF transcription factors, revealing common regulatory features of C4 evolution.

The study uses an imputation strategy that integrates deep single-cell RNA sequencing with spatial gene expression data to map transcriptional dynamics across barley inflorescence development at cellular resolution. By leveraging the BARVISTA web interface, the authors identify key transcriptional events in meristem founder cells, characterize complex branching mutants, and reconstruct spatio‑temporal trajectories of flower organogenesis, offering insights for targeted trait manipulation.

The study finely dissected shoot stem cell–enriched tissues from maize and Arabidopsis thaliana and optimized single‑cell RNA‑seq protocols to reliably capture CLAVATA3 and WUSCHEL‑expressing cells. Cross‑species comparison and functional validation, including spatial transcriptomics and mutant analyses, revealed conserved ribosome‑associated RNA‑binding proteins and sugar‑kinase families as key regulators linked to shoot development and yield traits.

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.