The study reveals that whole‑seedling transcriptomic analyses of Arabidopsis thermomorphogenesis are highly variable and often mask organ‑specific responses, with nearly 70% of differentially expressed genes in whole seedlings not detected in any dissected organ. By directly comparing RNA‑seq from whole seedlings and individual organs (root, hypocotyl, cotyledon) and supporting the findings with proteomics, the authors demonstrate that pooling tissues confounds gene‑regulation insights and call for organ‑level approaches in future warm‑temperature research.

The study applied a progressive, sublethal drought treatment to Arabidopsis thaliana, collecting time‑resolved phenotypic and transcriptomic data. Machine‑learning analysis revealed distinct drought stages driven by multiple overlapping transcriptional programs that intersect with plant aging, and identified high‑explanatory‑power transcripts as biomarkers rather than causal agents.

Salt stress strongly suppresses root growth in Festuca rubra while sparing shoot development. Transcriptome profiling identified over 68,000 differentially expressed genes, with up‑regulated genes enriched in methionine, melatonin, and suberin biosynthesis and down‑regulated genes involved in gibberellin, ABA, and sugar signaling, indicating extensive hormonal and metabolic reprogramming. Paradoxical regulation of gibberellin and ethylene pathways suggests a finely tuned balance between growth and stress responses.

The study examined how single and repeated mechanical disturbances (whole‑pot drops) affect leaf folding in Mimosa pudica, using chlorophyll fluorescence to track photosystem II efficiency and transcriptome profiling to identify responsive genes. A single drop mainly up‑regulated flavonoid biosynthesis genes, whereas multiple drops triggered broader biotic and abiotic stress pathways, indicating a shift in the plant’s gene regulatory network under repeated stress.

The study characterized the virome of Tamarillo (Solanum betaceum) across eight locations in Narino, Colombia, revealing up to four virus species from the Torradovirus, Potyvirus, and Polerovirus genera, including the first report of a torradovirus in tamarillo. A novel isolate of potato virus Y‑Tamarillo (PVY‑Tam) with unique P3N‑PIPO protein truncations was identified, suggesting host‑specific adaptation and informing future diagnostic and control strategies.

The study used RNA‑seq to compare early transcriptional responses to acute heat and cold stress in cultivated cranberry (Vaccinium macrocarpon) and its F1 hybrids with the cold‑adapted wild relative V. oxycoccos. Cold stress triggered differential expression in pathways such as photosynthesis, ribosomes, defense, and hormone signaling, with some hybrids showing transiently elevated cold‑responsive expression, suggesting potential cold‑tolerance introgression. The results highlight the utility of wild germplasm for breeding temperature‑resilient cranberries.

The study shows that inoculating Arabidopsis thaliana with the plant‑growth‑promoting bacterium Enterobacter sp. SA187 markedly boosts root and shoot biomass under elevated CO₂, accompanied by altered nitrogen and carbon content and reshaped phytohormone signaling. Transcriptomic and metabolomic analyses reveal activation of salicylic acid, jasmonic acid, and ethylene pathways and enhanced primary metabolism, while the ethylene‑insensitive ein2‑1 mutant demonstrates that the growth benefits are ethylene‑dependent.

The study examined soybean (Glycine max) responses to simultaneous drought and Asian soybean rust infection using combined transcriptomic and metabolomic analyses. Weighted Gene Co-expression Network Analysis identified stress-specific gene modules linked to metabolites, while Copula Graphical Models uncovered sparse, condition‑specific networks, revealing distinct molecular signatures for each stress without overlapping genes or metabolites. The integrative approach underscores a hierarchical, modular defense architecture and suggests targets for breeding multi‑stress resilient soybeans.

The study identifies the pseudokinase CRN in Medicago truncatula as a regulator of inflorescence meristem branching and a negative modulator of root interactions with arbuscular mycorrhizal (AM) fungi, operating partially independently of the AM autoregulation CLE peptide MtCLE53. Transcriptomic profiling of crn mutant roots reveals disruptions in nutrient, symbiosis, and stress signaling pathways, highlighting the multifaceted role of MtCRN in plant development and environmental interactions.

The study examined how varying temperature regimes, including cold deprivation and early cold exposure, affect dormancy onset and maintenance in sweet cherry (Prunus avium) flower buds. Phenological monitoring combined with transcriptomic analyses revealed that temperature drives dormancy progression, identifying specific genes and pathways responsive to cold, and uncovering a distinct shallow dormancy phase induced by cold deprivation with a unique molecular signature.