The study combined genomic and phenotypic approaches to investigate why polyploid grasses are abundant in North American prairies, focusing on the mixed‑ploidy grass Andropogon gerardi. A newly phased allopolyploid reference genome revealed that the hexaploid lineage arose during early Pleistocene glacial cycles, and that recurrent neopolyploidy (9x) events produce individuals with higher growth and reduced stomatal pore index, traits advantageous in xeric habitats, supporting both the opportunity and fitness‑advantage hypotheses for polyploid prevalence.

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 examines how ectopic accumulation of methionine in Arabidopsis thaliana leaves, driven by a deregulated AtCGS transgene under a seed‑specific promoter, reshapes metabolism, gene expression, and DNA methylation. High‑methionine lines exhibit increased amino acids and sugars, activation of stress‑hormone pathways, and reduced expression of DNA methyltransferases, while low‑methionine lines show heightened non‑CG methylation without major transcriptional changes. Integrated transcriptomic and methylomic analyses reveal a feedback loop linking sulfur‑carbon metabolism, stress adaptation, and epigenetic regulation.

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 integrated 16 Arabidopsis thaliana whole‑genome bisulfite sequencing datasets from 13 stress experiments using a unified bioinformatic pipeline to map common and stress‑specific DNA methylation changes. Differentially methylated regions varied by stress type and methylation context, with CG DMRs enriched in gene bodies and CHG/CHH DMRs in transposable elements, some of which overlapped loci prone to stable epimutations. Gene ontology and TE enrichment analyses highlighted shared stress pathways and suggest environmental stress can generate heritable epigenetic variation.

In a two-year controlled-environment experiment, diploid and tetraploid individuals of wild-type and cultivar Marshall annual ryegrass (Lolium multiflorum) were grown under elevated CO2 (540 vs 800 ppm) and differing evapotranspiration regimes. Elevated CO2 increased total biomass by 44% across ploidy levels, and tetraploid wild-type plants matched the improved cultivar in growth and forage quality, indicating that chromosome manipulation and wild genetic resources can enhance climate resilience.

High-quality PacBio HiFi draft genome assemblies were generated for three Bouteloua species (B. curtipendula, B. gracilis, B. eriopoda) with >98.5% BUSCO completeness. Gene prediction with Helixer produced inflated gene counts likely reflecting polyploidy and fragmented predictions, and panEDTA identified 25–40% transposable-element content dominated by LTR retrotransposons. These assemblies provide foundational references for comparative genomics within PACMAD grasses.

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 examined how the bioinoculant Trichoderma afroharzianum T22 influences Pisum sativum growth under iron-sufficient versus iron-deficient conditions, finding pronounced benefits—enhanced photosynthesis, Fe/N accumulation, and stress‑related gene expression—only during iron deficiency. RNA‑seq revealed distinct gene expression patterns tied to symbiosis, iron transport, and redox pathways, and microbiome profiling showed T22 reshapes the root bacterial community under deficiency, suggesting context‑dependent mutualism.