Identification of the RING-HCa E3 Ligase Gene Family and Functional Characterization of StDRIP1 in Potato Drought Stress Response

Genome-wide identification of the RLCK gene family in sugarcane and functional analysis of ScRLCK53 in salt tolerance.

First comprehensive characterization of the RLCK gene family in sugarcane is presented, elucidating its evolutionary features, expression dynamics and functional roles, and providing compelling evidence that ScRLCK53 modulates salt tolerance through activation of the JA signaling pathway.

Genome-wide characterization of the CIPK gene family in mung bean and functional validation of VrCIPK5 in drought stress response

The heterologous overexpression of VrCIPK5 in tobacco conferred enhanced drought tolerance by promoting proline accumulation, increasing antioxidant enzyme activities, accelerating stomatal closure, and upregulating downstream stress-responsive genes, thus alleviating reactive oxygen species overaccumulation and membrane lipid peroxidation.

Genome-wide identification and abiotic stress response analysis of the SUMO family in alfalfa (Medicago sativa L.)

SUMOylation is a well-conserved post-translational modification that is essential for modulating plant adaptation to various abiotic stresses. Although the functions of small ubiquitin-like modifier (SUMO) genes have been reported in various plant species, systematic studies focusing on the SUMO gene family members in alfalfa remain limited. In this study, we identified 49 MsSUMO genes from the alfalfa genome using bioinformatics approaches, and conducted comprehensive analyses of their phylogenetic relationships, structural features, cis-regulatory elements, and expression patterns. Most MsSUMO genes were predicted to localize in the nucleus and cytoplasm, consistent with their roles in transcriptional regulation and protein modification. Phylogenetic analysis grouped MsSUMO, soybean and Arabidopsis SUMO genes into seven subfamilies, which exhibited both high homology and species-specific divergence, suggesting functional differentiation during evolution. Conserved motif and domain analyses revealed strong structural consistency among MsSUMO members, with relatively simple gene architectures. In total, 59 types of cis-elements were detected in the promoter regions, playing crucial roles in plant growth, light signaling, and responses to biotic and abiotic stresses. Abscisic acid-responsive elements (ABREs) were the most abundant, implying that this gene family may serve key functions in stress regulation via the abscisic acid (ABA) signal pathway. Protein interaction network analysis indicated that MsSUMO members cooperate with core enzymes to modulate downstream stress-responsive targets. Transcriptome and real-time quantitative polymerase chain reaction (RT-qPCR) results showed that eight MsSUMO genes exhibited significant expression responses to salt, drought, and waterlogging stresses. Remarkably, six genes consistently exhibited upregulation across all three stress conditions. This observation underscores their potential as pivotal players in abiotic stress tolerance and identifies them as promising candidates for subsequent functional characterization.

Genome-wide identification of the SnRK2 gene family and its response to drought stress in Bombax ceiba

Introduction Drought is a major abiotic stress limiting the growth and ecological adaptation of tropical and subtropical trees. The SnRK2 gene family is a core regulator in ABA signaling and drought response pathways. However, genome-wide identification and functional characterization of the SnRK2 family remain unclear in Bombax ceiba, a typical drought-tolerant tropical pioneer tree species with important ecological and economic value. Methods We performed genome-wide identification of the BcSnRK2 gene family using bioinformatics approaches. Phylogenetic relationships, gene structures, conserved motifs, cis-acting elements, chromosomal localization, and protein structures were systematically analyzed. Subcellular localization was verified by transient expression in Nicotiana benthamiana. Tissue-specific expression and drought-responsive patterns were detected by qRT-PCR under 10% PEG6000 treatment. Protein–protein interaction networks were predicted using the STRING database. Results A total of nine BcSnRK2 genes were identified and unevenly distributed across eight chromosomes. All BcSnRK2 proteins contained conserved kinase domains and shared a highly conserved exon–intron structure. Promoter regions harbored abundant ABA-responsive and stress-related cis-elements. BcSnRK2 genes exhibited distinct tissue-specific expression profiles. All genes were significantly induced by drought stress in a tissue- and time-dependent manner, with BcSnRK2.9 and BcSnRK2.7 showing strong and sustained activation in shoots and BcSnRK2.7 and BcSnRK2.3 responding prominently in roots. BcSnRK2 proteins were localized in the cytoplasm, plasma membrane, and nucleus, and were predicted to interact with core components of the ABA signaling pathway. Discussion The BcSnRK2 family exhibits evolutionary conservation and functional divergence in Bombax ceiba. The compact size of the SnRK2 family, conserved structural features, and distinct tissue-specific drought response patterns are consistent with a streamlined stress signaling system that may contribute to the ecological adaptation of Bombax ceiba in seasonally dry tropical environments, although formal evolutionary analyses are required to establish adaptive significance. This study provides valuable gene resources for drought resistance breeding of woody plants and advances the understanding of stress signaling mechanisms in tropical trees.

Characterization, evolution, and expression profiling of cotton DUF677 protein family and their potential role in drought and salt stress response

The membrane-bound proteins belonging to DUF677 (domain of unknown function 677) are found mainly in green plants. The function of the DUF677 gene (AT14A) has been investigated in Arabidopsis and tomato in relation to drought stress tolerance. Overexpression of AT14A improves drought tolerance in tomato, promotes growth in Arabidopsis during drought stress, and confers tolerance against oxidative damage caused by drought stress in suspension-cultured A. thaliana. However, the role of the DUF677 gene family has not yet been reported in cotton. We identified 148 DUF677 genes from 15 selected plant species using domain-based and homology-supported bioinformatics approaches and classified them into two major groups (I and II) based on phylogenetic analysis. Group I is further divided into two sub-groups (IA and IB). Structural analysis revealed the presence of a few introns in the DUF677 genes. The evolution and expansion of the DUF677 protein family were primarily driven by segmental duplication. Seventy-one miRNAs were predicted to target 29 GhDUF677 genes, including Ghi-MIR397, Ghi-MIR8722, and Ghi-MIRN1429. Several cis-elements, such as MBS, ABRE, TCA elements, and W-Box, which were known to play a role in abiotic stress response, were observed in the promoter region of GhDUF677 genes. RNA-seq data were analyzed for tissue-specific expression, and qRT‒PCR was performed on six selected genes. The outcomes revealed high levels of GhDUF677 gene expression across different tissues under abiotic stress conditions. This study provides a genome-wide bioinformatics and expression-based characterization of the DUF677 gene family in cotton, identifying candidate genes potentially associated with drought and salt stress responses. While the findings are based on evolutionary, regulatory, and transcriptomic evidence, they do not constitute direct functional validation. Instead, this study establishes a theoretical and genomic foundation for future functional studies aimed at elucidating the precise roles of DUF677 genes in cotton stress tolerance.

Comprehensive genome-wide analysis of DUF668 gene family in potato reveals roles in growth and stress responses.