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 researchers performed a large‑scale field trial with 105 wheat (Triticum aestivum) genotypes inoculated by Fusarium culmorum, combining quantitative deoxynivalenol (DON) profiling and untargeted metabolomics to uncover molecular signatures of infection. Sesquiterpene‑derived metabolites tracked toxin accumulation, whereas glycosylated diterpene conjugates were enriched in low‑DON samples, indicating a potential defensive metabolic pathway.

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.

Integrating physiological, transcriptomic, and cellular analyses, the study shows that olive fruit abscission zones undergo lignification, alkalization, and extensive cell‑wall remodeling during natural maturation and after ethephon treatment. A set of 733 FAZ‑specific genes, including β‑1,3‑glucanases, pectate lyases, and pH‑regulating transporters, were identified, and increased glucanase activity together with reduced plasmodesmata callose suggest enhanced intercellular communication facilitates organ detachment in this non‑climacteric fruit.

The study uses a multi‑omics strategy to chart transcriptomic and epigenomic changes throughout pepper (Capsicum) fruit pericarp development and ripening, linking chromatin accessibility, H3K27ac/H3K27me3 dynamics, and global DNA demethylation to transcriptional reprogramming. Network analysis suggests that ripening regulators known from climacteric tomato also function in non‑climacteric pepper, and epigenetic regulation of carotenoid and vitamin C biosynthesis pathways is detailed.

The study mapped the cis‑regulatory landscape of the winter rapeseed cultivar Express617, identifying thousands of novel regulatory elements and characterizing super‑enhancers that are asymmetrically enriched in the Cn subgenome of Brassica napus. An in‑silico pipeline combining population‑level expression data and machine‑learning models revealed that many SE‑associated genes are expressed above predicted levels, and structural variants disrupting SEs lead to reduced gene expression, highlighting their functional importance for gene regulation and breeding.

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 investigates the wheat Pm3 NLR allelic series, revealing that near-identical Pm3d and Pm3e alleles confer broad-spectrum resistance by recognizing multiple, structurally diverse powdery mildew effectors. Using chimeric NLR constructs, the authors pinpoint specificity-determining polymorphisms and demonstrate that engineered combinations of Pm3d and Pm3e further expand effector recognition, showcasing the potential for durable wheat protection through NLR engineering.