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 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 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.

Phylogenetic analysis reveals that non‑seed plants, exemplified by the liverwort Marchantia polymorpha, possess a streamlined repertoire of cyclin and CDK genes, with only three cyclins active in a phase‑specific manner during vegetative development. Single‑cell RNA‑seq and fluorescent reporter assays, combined with functional overexpression studies, demonstrate the distinct, non‑redundant roles of MpCYCD;1, MpCYCA, and MpCYCB;1 in G1 entry, S‑phase progression, and G2/M transition, respectively.

The study combined single-molecule fluorescence in situ hybridization (smFISH) and single-cell RNA sequencing (scRNA-seq) to map cell-type specific gene expression during early wheat spike development, profiling over 48,000 cells and identifying 21 spatial expression domains and 23 scRNA-seq clusters. Functional validation using induced mutants linked distinct expression patterns of LFY, SPL14, and FZP to specific meristematic regions, and imputed transcriptomes enabled the discovery of co‑expressed genes and gene networks governing spike formation.