The study used untargeted metabolomics and QTL mapping in a tomato recombinant inbred line population to characterize root exudate composition and identify genetic loci controlling specific metabolites. It reveals domestication-driven changes in exudate profiles and links metabolic QTLs with previously reported microbial QTLs, suggesting a genetic basis for shaping the root microbiome.

Using ten Phaeodactylum tricornutum mutant strains with graded constitutive Lhcx1 expression, the study links NPQ induction under high light to physiological outcomes (oxidized QA, increased cyclic electron flow) and extensive transcriptomic reprogramming, affecting nearly half the genome. The approach demonstrates that higher NPQ mitigates PSII damage, boosts ATP production for repair, and drives distinct gene regulatory networks, providing a model framework for dissecting photosynthetic and gene expression integration.

The study establishes a tractable system using the large bloom-forming diatom Coscinodiscus granii and its natural oomycete parasite Lagenisma coscinodisci, enabling manual isolation of single host cells and stable co-cultures. High‑quality transcriptomes for both partners were assembled, revealing diverse oomycete effectors and a host transcriptional response involving proteases and exosome pathways, while also profiling the co‑occurring heterotrophic flagellate Pteridomonas sp. This tripartite platform provides a unique marine model for dissecting molecular mechanisms of oomycete‑diatom interactions.

The study generated an integrated single‑nucleus RNA‑seq and chromatin accessibility (snATAC‑seq) dataset from soybean roots infected with soybean cyst nematodes, profiling over 56,000 nuclei and uncovering distinct syncytial subpopulations with a procambium signature. Analyses revealed transcriptional programs and TF motifs (e.g., CAMTA1 repression of defense genes, MYB and E2F activation of cell‑wall remodeling and DNA replication) underlying syncytium initiation, immune suppression, cell fusion, and endoreduplication.

The study evaluated a transgenic soybean line (VPZ-34A) expressing Arabidopsis VDE, PsbS, and ZEP for combined improvements in light‑use efficiency and carbon assimilation under ambient and elevated CO2 in a FACE experiment. While VPZ‑34A showed enhanced maximum quantum efficiency of PSII under fluctuating light, it did not increase carbon assimilation efficiency or yield, and transcriptome analysis revealed limited gene expression changes. The results suggest that VPZ‑mediated photosynthetic gains are insufficient to boost productivity under elevated CO2.

The study investigates the molecular basis of heat‑tolerant pollen tube growth in tomato (Solanum lycopersicum) by comparing thermotolerant and sensitive cultivars. Using live imaging, transcriptomics, proteomics, and genetics, the authors identified the Rapid Alkalinization Factor (RALF) signaling pathway as a key regulator of pollen tube integrity under high temperature, with loss of a specific RALF peptide enhancing tube integrity in a thermotolerant cultivar.

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 examined drought tolerance across nine provenances of the conifer Pinus nigra using high‑throughput phenotyping combined with metabolomic and transcriptomic analyses under controlled soil‑drying conditions. Drought tolerance, measured by the decline in Fv/Fm, varied among provenances but was not linked to a climatic gradient and was independent of growth, with tolerant provenances showing distinct flavonoid and diterpene profiles and provenance‑specific gene expression patterns. Integrating phenotypic and molecular data revealed metabolic signatures underlying drought adaptation in this non‑model conifer.

The study applied limited proteolysis‑coupled mass spectrometry (LiP‑MS) to map JA‑protein interactions, validating known JA binders and uncovering novel candidates, including several UDP‑glucuronosyltransferases (UGTs). Functional omics, biochemical, enzymatic, and structural analyses demonstrated that two tomato UGTs glucosylate jasmonic acid, revealing a previously missing step in JA catabolism.

The study applied single-nucleus RNA sequencing to Sorghum purpureosericeum embryos undergoing B‑chromosome elimination, revealing a greater repertoire of B‑linked transcripts than previously reported. Nuclei containing B‑specific transcripts formed a distinct cluster (cluster 10) that split into two subpopulations with divergent transcriptional profiles, suggesting one subpopulation prepares for elimination while the other maintains normal segregation. These findings demonstrate the power of single‑cell approaches to dissect the dynamic behavior of supernumerary chromosomes during development.