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.
Abstract
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.
A genome-wide identification and comparative analysis of the CSP gene family in yak is performed primarily using bioinformatics approaches based on publicly available genomic and transcriptomic datasets, along with a preliminary validation of their differential expression under cold and hypoxic stress.
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.
Ting Wang, Yupeng Guo, Yi Xu et al.· PeerJ· 0 citations
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.
Sheraz Ahmad, Huimin Song, Hangbo Cao et al.· International Journal of Mol...· 0 citations
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.
Yu-Mei Shi, Zhifang Zhang, Ruoxin He et al.· Frontiers in Plant Science· 0 citations
Nuclear Factor Y, subunit A (NFYA) constitutes a family of transcription factors that play critical roles in plant growth, development and abiotic stress responses. Taxodium hybrid ‘Zhongshanshan’ (T. mucronatum × T. distichum) is a fast-growing tree species with high industrial value and remarkable flooding tolerance. However, the systematic characteristics and abiotic stress response patterns of the ThNFYA gene family remain unclear. In this study, a total of 11 ThNFYA genes were identified. The encoded proteins ranged from 67 to 372 amino acids in length, with predicted molecular weights between 16.84 and 40.12 kDa. Phylogenetic analysis classified plant NFYAs into four clades, with all ThNFYAs falling into clades I and IV. Expression profiling revealed tissue-specific patterns, with six members showing the highest transcript levels in the cambium. Multiple cis-acting elements associated with stress and hormone responses were detected in the promoter regions of ThNFYAs. Most ThNFYAs were differentially regulated under salt, drought, and flooding stresses. Notably, most clade IV members (ThNFYA3, ThNFYA4, and ThNFYA6-ThNFYA8) were downregulated in the wood under partial submergence. This indicates their potential role in modifying wood properties in response to flooding. Co-expression network analysis identified ThNFYA1 and ThNFYA8 as central hub genes in leaves under partial submergence. Overall, these results suggest that the ThNFYA family may serve as candidate regulators of development and stress adaptation in T. hybrid ‘Zhongshanshan’. This study provides valuable insights for further functional verification of ThNFYAs and lays a foundation for marker-assisted breeding of stress-tolerant varieties.
Coffee is a livelihood source for millions of farmers and plays a significant role in the economy of many coffee-producing countries. Abiotic stresses, such as drought and high temperature, however, negatively impact coffee growth, productivity, and bean quality. Heat shock factors (HSFs) play a crucial role in the plant response to heat and other abiotic stresses. However, there is still not a lot of detailed knowledge about the HSF gene family in Coffea arabica. In this study, a genome-wide search was performed to find and characterize the genes of HSF from C.arabica. A total of 59 putative CaHSF genes have been identified and characterized according to their physicochemical properties, chromosomal distribution, gene structure, conserved motifs, phylogenetic relationship, duplication event, synteny, cis-regulatory elements, and protein–protein interactions. The genes identified for CaHSF were assigned to different scaffolds of the genome, and they had different sizes, molecular mass, isoelectric point, GRAVY value, and aliphatic index of their protein. Through the relationships induced by the phylogenetic and conserved-domain analyses, and by their conservation, it was possible to get insight into the evolution of the proteins of the CaHSF family. Abiotic stress response, hormone signaling, and light regulation were noted to have several cis-regulatory elements associated with them in the promoter analysis and hence the possible role of the CaHSF genes in stress adaptation. Duplication and synteny analyses also showed that gene duplication played a role in the diversification and expansion of the CaHSF gene family in C. arabica. Overall, this study is a thorough genomic analysis of the CaHSF gene family, which can serve as a basis for future functional studies for understanding the molecular mechanism of abiotic stress tolerance in coffee.
S. Naeem, Z. Ali, Z. Naeem et al.· Bulletin of Biological and A...· 0 citations
