Comparative Phylogenomics and Transcriptional Regulatory Networks of AQPs, HSPs, and LEA Proteins in Salt-Stressed Portulaca oleracea.

Genome-Wide Characterization of the ZIP Transporter Family in Sea Island Cotton (Gossypium barbadense L.) and Expression Profiling Under Heavy Metal and Pathogen Stresses

Simple Summary Sea Island cotton (Gossypium barbadense L.) is widely cultivated for its high-grade extra-long staple fiber and excellent disease resistance. However, its cultivation is increasingly threatened by soil heavy metal contamination (such as cadmium toxicity) and fungal diseases (such as Verticillium wilt caused by Verticillium dahliae). Zinc/iron-regulated transporter-like proteins (ZIPs) serve as essential membrane transporters that manage transition metal homeostasis and modulate stress responses in plants. In this study, we systematically identified 46 GbZIP genes across the G. barbadense genome and comprehensively evaluated their structural characteristics, evolutionary origin, cis-regulatory elements, and expression patterns. Transcriptional analysis demonstrated that several key GbZIP members dynamically respond to cadmium exposure, fungal infection, and their combined occurrence. These findings highlight crucial candidate genes for molecular breeding aimed at improving stress resilience and metal tolerance in premium cotton germplasm.

Integrative Multi-Scale Analysis Identifies the Hub Gene TRE1 Associating Trehalose Metabolism With Salinity Tolerance in Rice.

Salinity is a major constraint on rice (Oryza sativa L.) production, yet the regulatory hubs that distinguish tolerant from susceptible genotypes remain largely unknown. Using a computational and experimental pipeline combining time-series meta-transcriptomics, weighted gene co-expression network analysis (WGCNA), fuzzy clustering, network centrality metrics, promoter analysis, and molecular and physicochemical evaluations, we identified genotype-specific hub genes associated with salinity tolerance in rice. Analysis of RNA-Seq data from tolerant (Pokkali) and susceptible (IR29) genotypes across five time points after salinity treatment yielded 3369 meta-differentially expressed genes. WGCNA revealed a salinity-responsive co-expression module, within which fuzzy clustering uncovered a cluster of 48 genes showing striking opposite temporal patterns between genotypes. Multi-metric centrality ranking prioritized Trehalase1 (TRE1), encoding a trehalase enzyme, among the identified hub genes. Promoter analysis of TRE1 revealed the presence of stress-related cis-elements (ABRE, TGACG-motif, MYB/MYC, DRE). Independent greenhouse validation confirmed the opposite expression pattern of TRE1 between Pokkali and IR29 under salinity, correlating with increased trehalose accumulation in Pokkali and trehalose depletion in IR29. Physicochemical assessments showed that Pokkali exhibited lower oxidative stress markers, higher relative water content, better photosynthetic performance, and a more favorable K+/Na+ ratio than IR29. Principal component analysis distinctly separated the two genotypes, with TRE1 expression clustering with susceptibility-associated traits, while trehalose clustered with tolerance-associated traits. Our network-based discovery and experimental validation together indicate that the contrasting regulation of the hub gene TRE1 links trehalose metabolism to salinity tolerance in rice, highlighting TRE1 as a possible target for further functional analysis to enhance salinity tolerance.

Transcriptomic insights into renal osmoregulation and environmental adaptation in two hammerhead shark species (Sphyrna zygaena and Sphyrna lewini)

Phylogenomics and expression profiling of wheat (Triticum aestivum L.) magnesium transporters under dual drought and salinity stress conditions

The expression analysis of TaMGT genes shows coordinated but differential induction under combined drought and salinity stress, with core members broadly activated and others displaying tissue-specific responses, underscoring their roles in Mg2⁺ homeostasis while cautioning that double-stress specificity remains unverified without single-stress comparisons.

Proteomic Insights into Salt-Stress Tolerance in Zygosaccharomyces rouxii Revealed by Data-Independent Acquisition Mass Spectrometry.

Under severe stress, GO and KEGG enrichment consistently revealed the reinforcement of central carbon and energy metabolism, peroxisome-associated fatty acid turnover, oxidoreductase/redox activities, and translation and nucleotide metabolic pathways.

Selaginella sellowii gene regulatory networks reveal distinct transcriptional strategies for dehydration stress and recovery.

Vegetative desiccation tolerance (VDT) enables resurrection plants to withstand extreme water loss, yet its system-level regulation remains incompletely understood. Here, we interrogated the VDT landscape in Selaginella sellowii using time-series RNA-seq and a computational pipeline that integrates ensemble network inference, graph attention networks (GATs), and protein language models (PLMs). Specifically, we captured the transcriptional response to water potentials characteristic of resurrection plants but lethal to most species, including -4, -10, and -150 MPa. Our analysis revealed two distinct strategies for dehydration tolerance based on stress severity. Intermediate dehydration elicits a complex transcriptional response associated with active damage control, while extreme dehydration shifts to a minimalist, stable transcriptome. Network analysis identified 12 persistent regulators bridging quiescence and recovery. GAT embedding further demonstrated that these regulators undergo context-specific functional reprogramming to drive rapid cellular reconstruction. This study establishes a regulatory blueprint for VDT, identifies key mechanisms linking quiescence to coordinated recovery, and provides a robust methodological framework for decoding complex gene regulatory networks (GRNs).