Phosphite (Phi) and phosphate (Pi) share the same root uptake system, but Phi acts as a biostimulant that modulates plant growth and disease resistance in a species‑ and Pi‑dependent manner. In Arabidopsis, Phi induces hypersensitive‑like cell death and enhances resistance to Plectosphaerella cucumerina, while in rice it counteracts Pi‑induced susceptibility to Magnaporthe oryzae and Fusarium fujikuroi, accompanied by extensive transcriptional reprogramming.

The authors compiled and standardized published data on Rubisco dark inhibition for 157 flowering plant species, categorizing them into four inhibition levels and analyzing phylogenetic trends. Their meta‑analysis reveals a complex, uneven distribution of inhibition across taxa, suggesting underlying chloroplast microenvironment drivers and providing a new resource for future photosynthesis improvement efforts.

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.

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.

The study uses a high‑throughput comparative multi‑omics strategy to profile transcript, metabolite, and protein dynamics in Arabidopsis thaliana seedlings throughout the heat‑stress memory (HSM) phase following acquired thermotolerance. Early recovery stages show rapid transcriptional activation of memory‑related genes, while protein levels stay elevated longer, and distinct metabolite patterns emerge, highlighting temporal layers of the memory process.

The study examines how the SnRK1 catalytic subunit KIN10 integrates carbon availability with root growth regulation in Arabidopsis thaliana. Loss of KIN10 reduces glucose‑induced inhibition of root elongation and triggers widespread transcriptional reprogramming of metabolic and hormonal pathways, notably affecting auxin and jasmonate signaling under sucrose supplementation. These findings highlight KIN10 as a central hub linking energy status to developmental and environmental cues in roots.

The study employed a multi‑omics workflow (transcriptomics, ribosome profiling, and proteomics) to uncover small peptides encoded by long non‑coding RNAs (LSEPs) in rice, finding that over 40% of surveyed lncRNAs associate with ribosomes. An optimized small‑peptide extraction followed by LC‑MS/MS identified 403 LSEPs, confirming the peptide‑coding capacity of plant lncRNAs and providing a scalable pipeline for large‑scale screening.

The study examined transcriptomic responses of the tropical seagrass Halophila stipulacea from a pristine and an impacted site under single and combined thermal and excess nutrient stress in mesocosms. Combined stress caused greater gene reprogramming than individual stresses, with thermal effects dominating and the impacted population showing reduced plasticity but higher resilience. Core stress‑response genes were identified as potential early field indicators of environmental stress.