The study examined three fruit morphotypes of the desert shrub Haloxylon ammodendron, revealing distinct germination performances under salt and drought stress. Proteomic analysis identified 721 differentially expressed proteins, particularly between the YP and PP morphotypes, linking stress‑responsive protein abundance to rapid germination in YP and delayed germination in PP as contrasting adaptive strategies. The findings suggest that fruit polymorphism facilitates niche differentiation and informs germplasm selection for desert restoration.

The study tracked molecular changes in plastoglobules and thylakoids of Zea mays B73 during heat stress and recovery, revealing increased plastoglobule size, number, and adjacent lipid droplets over time. Proteomic and lipidomic analyses uncovered up‑regulation of specific plastoglobule proteins and alterations in triacylglycerol, plastoquinone derivatives, and phytol esters, suggesting roles in membrane remodeling and oxidative defense. These insights highlight plastoglobule‑associated pathways as potential targets for enhancing heat resilience in maize.

The study used high-resolution chemical imaging to map cell-type specific metabolic changes in plant roots inoculated with a nine-strain endophyte consortium under drought, revealing that endophytes differentially alter root metabolomes across spatial domains. Machine learning identified metabolites and exudates predictive of drought and endophyte treatment, and correlation analyses showed dynamic endophyte–metabolite relationships under stress.

The study used transcriptomic and lipidomic profiling to investigate how chia (Salvia hispanica) leaves respond to short‑term (3 h) and prolonged (27 h) heat stress at 38 °C, revealing rapid activation of calcium‑signaling and heat‑shock pathways and reversible changes in triacylglycerol levels. Nearly all heat‑responsive genes returned to baseline expression after 24 h recovery, highlighting robust thermotolerance mechanisms that could inform improvement of other oilseed crops.

The study used Arabidopsis thaliana mutants with low (vtc2, vtc4) and high (vtc2/OE-VTC2) ascorbate levels to examine how ascorbate concentration affects gene expression and cellular homeostasis. Transcriptomic analysis revealed that altered ascorbate levels modulate defense and stress pathways, and that TAA1/TAR2‑mediated auxin biosynthesis is required for coping with elevated ascorbate in a light‑dependent manner.

The study introduces ENTRAP-seq, a high‑throughput in‑planta assay that couples protein‑coding libraries with a nuclear magnetic sorting‑based reporter to multiplexively assess transcriptional regulatory activity of thousands of protein variants. Using this platform and machine‑learning analysis, the authors screened 1,495 plant viral proteins, uncovering numerous novel regulatory domains, and applied machine‑guided, semi‑rational design to modify the activity of a plant transcription factor.

The study used phylogeny‑based analyses of 36 legume genomes and a newly created multiparent advanced generation intercross (MAGIC) population of common bean to predict and characterize genome‑wide deleterious mutations. Machine‑learning integration of conservation and protein features identified thousands of potentially deleterious sites, whose variation correlated negatively with flowering time, maturity, and yield, highlighting the impact of genetic load on breeding performance.

The authors introduce S²-PepAnalyst, a web-based tool that leverages plant-specific datasets and advanced machine learning to predict small signaling peptides (SSPs) with 99.5% accuracy and minimal false negatives. By integrating protein language models, geometric‑topological analysis, and reinforcement learning, the tool surpasses existing predictors such as SignalP 6.0 in classifying peptide families like CLE and RALF.

The study identifies the serine/threonine protein kinase CIPK14/SNRK3.15 as a regulator of sulfate‑deficiency responses in Arabidopsis thaliana seedlings, with mutants showing diminished early adaptive and later salvage responses under sulfur starvation. While snrk3.15 mutants exhibit no obvious phenotype under sufficient sulfur, the work provides a novel proteomic dataset comparing wild‑type and mutant seedlings under sulfur limitation.

The study performed daily large-scale glycome, transcriptome, and proteome profiling of developing fibers from the two cultivated cotton species, Gossypium barbadense and G. hirsutum, across primary and secondary cell wall stages. It identified delayed cellulose accumulation and distinct compositions of xyloglucans, homogalacturonans, rhamnogalacturonan‑I, and heteroxylans in G. barbadense, along with higher expression of specific glycosyltransferases and expansins, suggesting these molecular differences underlie the superior fiber length and strength of G. barbadense.