TL;DR
The results indicate that PvHsp90 genes are evolutionarily conserved and differentially regulated during heat stress, highlighting PvHsp90‑1 and PvHsp90‑2 as promising candidates for improving reproductive thermotolerance and heat resilience in common bean.
Abiotic stress severely limits plant growth and productivity. Taraxacum kok-saghyz Rodin (TKS), known for its environmental resilience, represents a valuable resource for identifying stress-tolerant genes to improve stress-adaptive crops. Plant AT-rich protein and zinc-binding protein (PLATZ) transcription factors serve as core regulators of plant growth, developmental processes, and adaptive responses to various stress conditions; however, they remain uncharacterized in TKS. Here, we identified 10 TksPLATZ genes through a whole-genome analysis. Phylogenetically, these genes were grouped into five distinct evolutionary branches. Promoter sequence analysis revealed multiple types of cis-acting regulatory elements that are connected with hormonal signal responses and environmental stress adaptation. Integrated analysis of transcriptome datasets and RT-qPCR validation demonstrated that TksPLATZ genes display tissue-specific expression profiles and show distinct responsive patterns to drought and salt stress treatments. Among them, TksPLATZ1, TksPLATZ2 and TksPLATZ7 were markedly induced under both stressors and were selected for further functional study. We demonstrated that TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively. Phenotypic data from overexpression experiments in plants confirm that heterologous expression of TksPLATZ1, TksPLATZ2, and TksPLATZ7 enhances the tolerance of Arabidopsis to salt and osmotic stress. These findings provide valuable genetic resources for improving plant tolerance to environmental stresses.
Simple Summary PLATZ transcription factors are a plant-specific family of zinc finger proteins that play important roles in regulating plant growth, development, and abiotic stress responses. In the legume model plant Medicago truncatula, the PLATZ gene family has not been systematically characterized. In this study, a total of 16 MtPLATZ genes were identified in the M. truncatula genome and classified into four distinct subgroups based on phylogenetic analysis. This family includes five segmental duplication pairs and one tandem duplication pair, all of which have Ka/Ks ratios less than 1, indicating that MtPLATZ genes have experienced strong purifying selection during evolution. Cis-acting element analysis revealed that the promoter regions of MtPLATZ genes contain multiple stress-responsive and hormone-responsive elements, suggesting their potential extensive involvement in environmental adaptation. Preliminary expression profiling under various abiotic stresses, including PEG-induced osmotic stress, acute NaCl shock, acute heat shock, and acute cold shock, demonstrated that MtPLATZ genes exhibit treatment-specific and time-dependent expression patterns, indicating that they may have functional divergence. This study provides a systematic analysis of the MtPLATZ gene family in M. truncatula, offering a valuable reference for functional studies and genetic improvement of stress tolerance in legumes.
GATA transcription factors represent a conserved family of regulatory proteins that modulate plant growth and stress adaptation. While GATA families have been well characterized in model plants and Solanaceae crops, their evolutionary and functional features remain poorly defined in eggplant (Solanum melongena L.). Here, we systematically characterized the SmGATA gene family using the latest eggplant V4.1 reference genome and multi-stress transcriptome data. A total of 29 SmGATA genes were identified, with segmental duplication predominantly driving family expansion under strong purifying selection. Cross-species synteny analysis revealed high conservation of GATA homologs within Solanaceae species. Phylogenetic clustering divided SmGATA genes into four subfamilies, whose members exhibited conserved gene structures and motif compositions. Numerous cis-acting elements associated with plant growth, phytohormone signaling, and stress responses were enriched in SmGATA promoters. Tissue-specific expression analysis demonstrated the extensive involvement of SmGATA genes in eggplant organ development. Combined transcriptome screening and qRT-PCR validation identified multiple stress-responsive SmGATA members. Notably, SmGATA5 showed differential expression under high- and low-temperature conditions, and SmGATA17 exhibited the broadest spectrum of responses to abiotic and biotic stresses. This study elucidates the evolutionary conservation and functional diversity of the eggplant GATA family, providing valuable candidate genes for future functional research and stress-tolerant molecular breeding in eggplant.
Rising temperatures pose daunting challenges for sustainable yield and nutritional quality of rice (Oryza sativa L.), thus putting food security at risk. Limited information exists regarding cis-acting regulatory elements and candidate genes controlling the heat shock transcription factor (HSF) gene family in rice. Therefore, the present study identified HSF genes in the japonica (Nipponbare) and indica (9311) rice cultivars through in silico repositories. Three candidate genes (HSFC2B, HSFB1, and HSFC2A) were selected for qRT-PCR analysis to validate their expression patterns under heat stress (HS). The present findings reported a total of 25 OsHSF genes through in silico genome-wide identification. Comparative analysis illustrated that the OsHSF genes had structural similarities but different expression and transcriptional regulation between the two cultivars. HSF genes were unevenly distributed across the 12 rice chromosomes, suggesting that tandem duplication and gene repetition may have contributed to the evolution of novel genes. Phylogenetic analysis revealed that all OsHSF gene family members have shared common ancestry, but several genes lack introns, potentially facilitating swift stress responses as indicated by gene structure analysis. Expression analysis revealed that candidate genes were active, with HSFC2A exhibiting the highest level of expression in the japonica cultivar compared to indica under heat-stressed conditions. HSFC2B gene showed a higher statistical difference in its response between cultivars, time points, and cultivar vs. time points interactions compared to HSFC2A and HSFB1. These findings offer valuable insights into the function of OsHSF genes that will contribute to the development of climate-resilient rice cultivars.
Proper protein folding and stability are vital for plant development and stress tolerance. Heat shock proteins (Hsps), regulated by heat shock transcription factors (Hsfs), play a central role in abiotic stress responses. Zucchini (Cucurbita pepo), a key member of the Cucurbitaceae family, is economically important and widely cultivated worldwide. In Turkey, Seyden F1 and Cordelia F1 are the predominant cultivars used for domestic consumption and export. In this study, a total of 464 C. pepo Hsp genes distributed across six subfamilies and 77 CpHsf genes were identified and analyzed using bioinformatics tools, representing the first comprehensive genome-wide identification and characterization of Hsp and Hsf gene families in C. pepo across two cultivars. Gene structure, conserved motifs, and phylogenetic relationships indicated strong evolutionary conservation, largely shaped by segmental duplications. Comparative genomic analyses revealed that soybean is the closest species based on shared orthologs. miRNA analyses highlighted miR395 and miR167 as key post-transcriptional regulators of CpHsp and CpHsf genes. Transcriptomic analyses revealed distinct tissue-specific and temporal expression patterns under normal and stress conditions. qRT-PCR validation in Seyden F1 and Cordelia F1 cultivars under heat, drought, and combined stress treatments identified key stress-responsive genes, CpHsp70-20 and CpHsf-68, which were consistently upregulated across all stress conditions. Interestingly, CpHsp60-34 showed significant downregulation under heat stress in the Cordelia cultivar, highlighting genotype-specific variations between cultivars. The key marker genes and in silico interaction networks identified herein provide a robust resource for functional characterization and molecular breeding to improve stress resilience in zucchini.
Background/Objectives: Soybean (Glycine max) productivity is increasingly constrained by soil salinity. WIP transcription factors, a subfamily of C2H2-type zinc finger proteins, regulate cell division, differentiation, and tissue patterning in several plant species, but this gene family had not previously been systematically characterized in soybean or any other major legume crop. This study aimed to identify and characterize the GmWIP gene family genome-wide and evaluate its potential involvement in the soybean salt-stress response. Methods: Genome-wide identification of GmWIP genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4.ann1 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, and promoter cis-acting elements. Tissue-specific expression was examined using transcriptome data, and GmWIP responses to salt stress were profiled by RT-qPCR in roots, stems, and leaves of a salt-tolerant cultivar (HN531) and a salt-sensitive cultivar (HN563), alongside physiological measurements of oxidative stress and osmotic adjustment. Results: Thirty GmWIP genes were identified, with molecular weights from 26.90 to 57.52 kDa, distributed unevenly across 15 soybean chromosomes, with chromosomes 11, 12, and 13 forming a major hotspot (53.3% of the family). Duplication analysis detected 54 reconciled segmental duplicate gene pairs, all exhibiting Ka/Ks values < 1 (ranging from 0.0351 to 0.4471; mean 0.214), consistent with purifying selection acting on this gene set. GmWIP promoters were enriched for ABRE, MBS, and MeJA cis-acting elements. RT-qPCR showed genotype- and tissue-dependent differential expression under salt stress (e.g., up to 14.9-fold induction of GmWIP22 in HN531 stems), paralleled by superior proline accumulation (+45%), soluble sugars, and CAT activity (+38%) alongside reduced MDA accumulation in the tolerant cultivar. Conclusions: The GmWIP gene family has expanded substantially in soybean relative to previously characterized species and shows genotype-dependent transcriptional responses to salt stress, suggesting that specific GmWIP members are candidate regulators of salt tolerance and warrant further functional investigation.