Genome-Wide Identification of the CaMED Gene Family in Pepper (Capsicum annuum L.) and Functional Characterization of CaMED25a in the Heat Stress Response

Genome-Wide Identification of the WOX Gene Family in Three Populus Species and Expression Profiling of Populus euphratica and Populus pruinosa Under Abiotic Stresses

The WUSCHEL-related homeobox (WOX) gene family plays crucial roles in plant growth, development, and stress responses. In this study, a comprehensive genome-wide analysis of WOX genes was conducted in three Populus species, P. euphratica, P. pruinosa, and P. deltoides. A total of 16, 16, and 21 WOX genes were identified, respectively, and classified into three clades (ancient, intermediate, and WUS/modern) based on phylogenetic relationships. Structural analyses revealed highly conserved homeodomain motifs and similar exon–intron organizations, indicating strong evolutionary conservation. Furthermore, synteny analyses demonstrated that whole-genome duplication or segmental duplication events were the primary drivers of WOX gene family expansion, with most duplicated gene pairs undergoing purifying selection. Promoter analysis identified abundant cis-acting elements related to light responsiveness, hormone signaling, and stress responses. Notably, transcriptomic profiling during seed germination under drought and salt stress revealed distinct interspecific expression patterns and temporal dynamics between the two desert poplars. Specifically, members such as PeWox11 and PpWox2 were significantly induced, suggesting their potential involvement in abiotic stress adaptation. These findings provide comprehensive insights into the evolutionary conservation and divergence of WOX genes in Populus, establishing a theoretical foundation for the molecular breeding of stress-tolerant woody plants.

Evolutionary Analysis and Expression Profiling of the TIFY Gene Family in Banana Under Multiple Stresses and Functional Characterization of MaTIFY20 in Drought Tolerance

The TIFY gene family comprises plant-specific transcriptional regulators central to jasmonic acid (JA) signaling and responses to biotic and abiotic stresses. Despite the economic importance of the banana (Musa spp.), the TIFY family remains largely uncharacterized in this crop. Here, we conducted a genome-wide identification and comprehensive analysis of the MaTIFY gene family in Musa acuminata. A total of 47 MaTIFY genes were identified, distributed across all 11 chromosomes. Phylogenetic analysis classified these into four subfamilies (TIFY, ZIZ/ZML, PPD, and JAZ), and conserved motif and domain analyses revealed a core TIFY domain architecture with subfamily-specific structural features. Gene Ontology (GO) enrichment and cis-acting regulatory element analyses suggested potential involvement in JA-mediated signaling, defense response, and hormone cross-talk. Expression profiling under drought, Fusarium oxysporum f. sp. cubense race 4 (Foc 4), and cold stress revealed distinct transcriptional responses, with MaTIFY5, MaTIFY16, MaTIFY20, MaTIFY26, and MaTIFY30 exhibiting enhanced induction in resistant cultivars compared to their susceptible counterparts. Functional characterization of MaTIFY20 confirmed its significant upregulation under drought stress and its ability to confer enhanced osmotic tolerance when heterologously expressed in yeast. These findings provide novel insights into the evolutionary dynamics and stress-responsive functions of banana TIFY genes and identify candidate targets for molecular breeding to improve abiotic and biotic stress resilience in banana.

Genome-Wide Identification and Stress Response Analysis of the GATA Gene Family in Eggplant (Solanum melongena L.)

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.

Unveiling the CpHsp and CpHsf Gene families in the zucchini genome: Evolution, structure, and stress-responsive expression

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.

Genome-Wide Identification of the SWEET Gene Family in Elymus nutans and Functional Characterization of EnSWEET15 in Salt Tolerance

The SWEET (Sugars Will Eventually be Exported Transporter) family, a class of sugar transporters identified in recent years, plays important roles in plant growth and development. Increasing evidence suggests that SWEET genes are also involved in plant responses to abiotic stresses, including salt stress. However, the genome-wide composition and salt-responsive functions of SWEET genes in Elymus nutans Griseb. have not been systematically characterized to date. This study presents the first genome-wide identification of the SWEET gene family in E. nutans and functional characterization of EnSWEET15 in salt stress response, providing candidate genes and a theoretical basis for improving salt tolerance in this species. A total of 12 EnSWEET genes were identified from the E. nutans genome and were unevenly distributed across eight chromosomes. Phylogenetic analysis classified them into four subfamilies, and promoter analysis revealed abundant cis-elements related to hormone signaling and stress responses, suggesting roles in abiotic stress adaptation. Expression analysis showed that EnSWEET15 was significantly upregulated in both roots and leaves under salt stress. The full-length EnSWEET15 coding sequence (930 bp ORF) was cloned and functionally characterized. Heterologous overexpression in Arabidopsis thaliana indicated that EnSWEET15 enhances salt tolerance. Transgenic lines showed reduced reactive oxygen species (ROS) accumulation and increased activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), compared with wild-type plants under salt stress. Overall, this study identifies EnSWEET15 as a positive regulator of salt tolerance via modulating ROS homeostasis, providing novel insights into SWEET-mediated salt stress response in perennial forages and valuable genetic resources for salt-tolerant breeding of E. nutans.

Genomic characterization, expression and functional analysis of the plant homeodomain (PHD) family in tomato (Solanum lycopersicum L.) under abiotic stresses