Four barley genotypes were examined under simultaneous Fusarium culmorum infection and drought, revealing genotype-dependent Fusarium Head Blight severity and largely additive transcriptomic responses dominated by drought. Co‑expression and hormone profiling linked ABA and auxin to stress‑specific gene modules, and a multiple linear regression model accurately predicted combined‑stress gene expression from single‑stress data, suggesting modular regulation.

The study examined nitrogen use strategies in the model alga Chlamydomonas reinhardtii by comparing growth on ammonium, nitrate, and urea, finding similar molar nitrogen utilization efficiency under saturating conditions. Rapid nitrogen uptake and storage were demonstrated through pulse experiments, and source‑specific transcriptome analysis revealed distinct regulation of assimilation pathways and transporters, supporting a model of flexible nitrogen acquisition and storage.

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 how maternal environmental conditions, specifically temperature and light intensity, influence seed longevity in eight Arabidopsis thaliana natural accessions. Seeds developed under higher temperature (27 °C) and high light showed increased longevity, with transcriptome analysis of the Bor-4 accession revealing dynamic changes in stored mRNAs, including upregulation of antioxidant defenses and raffinose family oligosaccharides. These findings highlight the genotype‑dependent modulation of seed traits by the maternal environment.

The study examined how polyploidy, hybridization, and incomplete lineage sorting affect phylogenetic reconstructions in the genus Packera, evaluating several published paralog‑processing pipelines. Results showed that the choice of orthology and paralog handling methods markedly altered tree topology, time‑calibrated phylogenies, biogeographic histories, and detection of ancient reticulation, underscoring the need for careful methodological selection alongside comprehensive taxon sampling.

The study evaluated whether integrating genomic, transcriptomic, and drone-derived phenomic data improves prediction of 129 maize traits across nine environments, using both linear (rrBLUP) and nonlinear (SVR) models. Multi-omics models consistently outperformed single-omics models, with transcriptomic data especially enhancing cross‑environment predictions and capturing genotype‑by‑environment interactions. The results highlight the added value of combining transcriptomics and phenomics with genotypes for more accurate and generalizable trait prediction in maize.

Using a controlled field experiment on clonal 35‑year‑old Norway spruce trees, the study examined molecular defense responses to Ips typographus attacks. A multi‑omics approach revealed rapid local increases in jasmonic acid and other phytohormones, leading to differential expression of up to 1,900 genes and corresponding proteomic and metabolomic changes that elevated deterrent compounds such as phenolic aglycones, diterpene resin acids, terpenes, and lignin.

The study investigates the evolutionary shift from archegonial to embryo‑sac reproduction by analyzing transcriptomes of Ginkgo reproductive organs and related species. It reveals that the angiosperm pollen‑tube guidance module MYB98‑CRP‑ECS is active in mature Ginkgo archegonia and that, while egg cell transcription is conserved, changes in the fate of other female gametophyte cells drove the transition, providing a molecular framework for this major reproductive evolution.

Using integrated metabolomics, fluxomics, and proteomics, the study shows that Bamboo mosaic virus infection in Nicotiana benthamiana redirects carbon flux toward glycolysis and the TCA cycle, enhancing mitochondrial metabolism. Silencing the mitochondrial NAD⁺-dependent malic enzyme 1 disrupts cytoplasmic NADH/NAD⁺ balance and alters defense gene expression, indicating that mitochondrial redox regulation is crucial for antiviral defense.

Foliar application of Trichoderma harzianum cell‑free culture filtrates (CF) increased fruit yield, root growth, and photosynthesis in a commercial tomato cultivar under prolonged water deficit in a Mediterranean greenhouse. Integrated physiological, metabolite, and transcriptomic analyses revealed that CF mitigated drought‑induced changes, suppressing about half of water‑stress responsive genes, thereby reducing the plant’s transcriptional sensitivity to water scarcity.