Search Results (2,837)

Background: Di19 (drought-induced 19)proteins belong to the C2H2-type zinc-finger family and play a crucial role in regulating plant growth, developmental processes, hormone signal transduction, and abiotic stress adaptation. However, research on the Di19 gene family in sweet potato and its diploid relatives remains relatively limited. Methods: At the whole-genome level, members of the Di19 gene family in sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30) were systematically identified, and multi-dimensional bioinformatics analyses were carried out. Results: Seven Di19 genes were identified per species, with the family’s overall evolutionary characteristics conserved. Some IbDi19s showed species-specific structural variations, mainly manifested as an increase in the number of exons, loss or substitution of conserved motifs. The expression patterns of Di19s of two diploid relatives are highly conserved. IbDi19s are mainly expressed in leaves and roots. Most members respond significantly to JA treatment, but hardly respond to IAA. The expression of IbDi19-1 was significantly up-regulated by 336-fold and 68-fold under GA3 and cold treatments, respectively. Based on bioinformatics and expression data, a hypothesis was proposed that IbDi19-1 may be involved in the regulation of low-temperature response and gibberellin signaling pathways. Conclusions: This study provides candidate genes and a theoretical basis for evolutionary analysis, stress-resistant molecular breeding of the Di19 gene family in sweet potato and its two diploid relatives. Full article

The Sugars Will Eventually be Exported Transporters (SWEET) family plays a crucial role in the carbohydrate distribution, phloem loading, and stress response of plants, yet the evolutionary characteristics and functional diversification of SWEET genes in the endangered timber species Phoebe bournei (Hemsl.) Yen C. Yang remain largely unexplored. In this study, 21 PbSWEET genes were identified and classified into four subfamilies (A-D). Subfamily A exhibited a unique lineage expansion, mainly driven by tandem and segmental duplications. The nonsynonymous-to-synonymous substitution ratio (Ka/Ks) values of all duplicate gene pairs were all less than 1, indicating a strong selective suppression effect; consistent with this evolutionary constraint, the majority of PbSWEET proteins harbor the conserved Medicago truncatula Nodulin 3/saliva (MtN3_slv) domain, with only a few exceptions lacking a complete version. Promoter and hormone response analyses revealed that under abscisic acid (ABA) stress, PbSWEET4 exhibited an immediate burst, whereas PbSWEET10 showed a delayed burst. Physiological data indicated that soluble sugars may be more dominant osmolytes than proline (Pro), a pattern that points to a potential carbon-centric regulatory strategy. PbSWEET4 showed an early burst before sugar/oxidative peaks, suggesting a possible non-canonical signaling role, whereas PbSWEET10 exhibited a late increase coinciding with sugar/malondialdehyde (MDA) peaks, suggesting potential involvement in sugar redistribution. Under methyl jasmonate (MeJA) treatment, PbSWEET10 was rapidly induced, yet sugar accumulation occurred only at 24 h, a temporal decoupling that suggests a possible transcription–metabolism decoupling. Collectively, these correlative patterns point to a possible dual-wave transcriptional mechanism and nominate PbSWEET10 as a candidate for stress response, though these inferences require functional validation. Full article

Citrus fruits are widely cultivated all over the world. Due to climatic conditions, citrus fruits are frequently exposed to periodic low temperatures, which poses a serious threat to their yield and quality. Cold not only restricts plant growth and deteriorates fruit quality but also leads to fruit abscission and tree mortality, posing severe constraints on large-scale citrus production. The TIFY family gene plays crucial roles in plant development and stress adaptation. However, the genome-wide identification and functional analysis of TIFY genes in cold stress adaptation of citrus plants remain largely unexplored. Here, we performed a systematic genome-wide analysis of the TIFY family in sweet orange (Citrus sinensis (L.) Osbeck) and identified 14 CsTIFY members. We conducted a comprehensive study on the protein characteristics, phylogenetic relationships, gene structure, chromosome distribution, promoter cis-acting elements, and subcellular localization of these genes. Phylogenetic analysis classified the CsTIFYs into ZML (ZML1–ZML4), JAZ (JAZ1–JAZ7), PPD (JAZ8, JAZ9), and TIFY (TIFY1) subfamilies, and they are distributed on seven chromosomes. Collinearity analysis revealed that segmental duplication is the primary driver for CsTIFY family expansion. Expression profiling under cold stress identified JAZ1, JAZ2, and JAZ3 as the most cold-inducible members. All three CsTIFY proteins are targeted to the nucleus, as confirmed by subcellular localization analysis. Overexpression of JAZ1, JAZ2, or JAZ3 in citrus calli significantly enhanced cold sensibility. Collectively, this study elucidates the gene function of CsTIFYs under cold stress and provides new insight for molecular breeding of cold-tolerant citrus varieties. Full article

Fragaria vesca is a highly adaptable diploid model species. Although bHLH transcription factors (TFs) have been widely reported to regulate plant development and stress responses, the bHLH gene family has not been systematically characterized in Fragaria vesca. In this study, we conducted a genome-wide analysis of the bHLH TF family based on the Fragaria vesca v6 genome assembly. A total of 117 FvbHLH genes were identified, and promoter analysis revealed the presence of numerous cis-regulatory elements associated with plant development, hormone signaling, and stress responses. Transcriptome analysis showed that several FvbHLH genes were differentially expressed in leaves and stems under low-temperature stress. The low-temperature expression patterns of selected genes were further validated by reverse transcription quantitative PCR (RT-qPCR). Moreover, heterologous overexpression of FvbHLH86 in Arabidopsis thaliana enhanced cold tolerance by improving reactive oxygen species (ROS) scavenging capacity. These findings provide a valuable foundation for future functional studies of FvbHLH genes and contribute to a better understanding of the molecular mechanisms underlying cold stress responses in Fragaria vesca. Full article

P. massoniana is an important native economic and ecological tree species in southern China, where seasonal drought has emerged as a critical factor limiting its productivity. The SAUR gene family, recognized as core early auxin-responsive genes, plays a crucial role in balancing plant growth, development, and stress adaptation; however, research related to this family in conifers remains limited. Utilizing the chromosome-level genome of P. massoniana, this study identified 73 SAUR genes (PmSAUR1~73) through bioinformatics methods, systematically analyzing the physicochemical properties of the encoded proteins, chromosomal localization, phylogenetic relationships, gene structures, and cis-acting elements. Combined with transcriptome sequencing and molecular experiments, the drought stress response patterns of these genes were further elucidated. The results indicated that PmSAUR genes predominantly encode alkaline proteins, primarily localized in mitochondria and nuclei, with an uneven distribution across nine chromosomes, where tandem duplication serves as the primary mechanism driving family expansion. Phylogenetic analysis classified these genes into seven subfamilies, which include both conserved clades homologous to angiosperms and branches specific to P. massoniana. All members contain the Auxin_inducible conserved domain, with motif1 identified as the core essential motif. Promoter regions were enriched with MeJA (methyl jasmonate)-responsive (56%), ABA-responsive, and drought stress-related cis-elements. Under drought stress, 38 PmSAUR genes exhibited diverse temporal expression patterns. Four key genes (PmSAUR14, PmSAUR28, PmSAUR54, and PmSAUR73), which are localized in the nucleus and exhibit high expression specifically in male cones or roots, were identified. These genes exhibit an expression pattern consistent with an auxin-negative response (i.e., repressed by IAA and induced by drought) and display a distinctive response pattern characterized by drought-induced upregulation coupled with IAA-mediated downregulation. This mechanism may contribute to the drought adaptation strategies of P. massoniana, involving regulatory processes for aboveground reproduction and adaptation of the underground root system. This study represents the first effort to elucidate the evolutionary characteristics and drought response patterns of the SAUR gene family in P. massoniana, thereby addressing the existing research gap regarding the functions of SAUR genes in coniferous trees. Furthermore, it offers candidate gene resources and theoretical support for the molecular breeding of stress resistance in P. massoniana. In addition, two auxin-induced SAUR genes (PmSAUR22 and PmSAUR37) were identified as contrasting examples, but the main focus of this study is on the four auxin-repressed genes. Full article

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) are plant-specific regulators involved in growth, development, and responses to abiotic stresses, yet their roles in halophytes remain largely unexplored. In this study, we performed a genome-wide identification of TCP family members in the extreme halophyte Salicornia europaea, uncovering 15 non-redundant genes (SeurTCPs) classified into PCF, CIN, and CYC/TB1 subfamilies. Gene structure and conserved motif analyses revealed that SeurTCPs are largely intronless and maintain the canonical TCP domain, while showing subfamily-specific variations in motif composition and secondary/tertiary structures. Promoter analysis identified abundant stress and hormone-responsive cis-elements, particularly ABRE and STRE, suggesting potential involvement in salt stress signaling. Protein–protein interaction network prediction highlighted CIN and PCF members as hub nodes, indicating central roles in growth and stress response regulation. Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis showed that most SeurTCP genes were responsive to salinity treatment, although the extent of transcriptional variation differed among subfamilies. Collectively, our results indicate that SeurTCPs balance conserved structural functions with subfamily-specific regulatory roles, contributing to S. europaea adaptation to extreme saline environments. This study provides valuable candidate genes for elucidating plant salt tolerance mechanisms and for potential crop improvement. Full article

Background: The NAC family constitutes one of the largest families of plant-specific transcription factors and plays crucial roles in fruit development, ripening, seed life, and stress responses. However, comprehensive characterization of NAC genes in Persea americana (avocado), an economically important horticultural crop, has been largely unexplored. Methods: We performed a genome-wide identification and systematic characterization of NAC transcription factor (TF) genes in P. americana using blastp analysis, phylogenetic reconstruction, expression profiling and weighted gene co-expression network analysis (WGCNA). Results: A total of 130 NAC genes (PaNACs) were identified and distributed across all 12 chromosomes. Phylogenetic analysis classified these PaNACs into eight distinct subfamilies. WGCNA identified 43 co-expression modules, with 68 PaNAC genes distributed across 24 modules associated with hormone signaling, cell wall modification, secondary metabolism, and fatty acid beta-oxidation. Among 48,785 developmental differentially expressed genes (DEGs), 70 PaNAC genes were differentially expressed, with PaNAC003 and PaNAC002 showing the strongest upregulation and PaNAC023 and PaNAC025 the strongest downregulation. Among 9488 ethylene-responsive DEGs, PaNAC041 was suppressed by ethylene and induced by 1-methylcyclopropene (1-MCP, a competitive inhibitor of ethylene perception), while PaNAC016, PaNAC085, and PaNAC086 showed the opposite pattern. Conclusions: These findings provide a genomic and transcriptional framework for future functional investigation of PaNAC genes and their potential relevance to avocado fruit development and postharvest ripening. Full article

Background: Uridine diphosphate glucose (UDP-Glc) is one of the key substrates for the biosynthesis of gallotannins in plants. UDP-glucose dehydrogenase (UGD) catalyzes the irreversible oxidation of UDP-Glc to UDP-glucuronic acid (UDP-GlcA), thus affecting the biosynthesis and accumulation of gallotannins in the Chinese gallnut. Methods and Results: In this study, we identified three members of the RcUGD family from the Rhus chinensis genome. Protein sequence alignment revealed that all three RcUGDs possess the conserved NAD⁺ coenzyme binding motif GAGYVGG and the catalytic motif GFGGSCFQKDIL. qRT-PCR analysis revealed that the expression levels of RcUGD3 in stem and root tissues were respectively 10-fold and 13-fold greater than that in the leaves, in which gallotannin accumulation was higher. RcUGD3 expression level declined by 63% during early (24 d) gallnut development, suggesting an inverse relationship between RcUGD3 expression level and gallotannin biosynthesis. In addition, subcellular localization analysis using the tobacco transient transformation system showed that RcUGD proteins are broadly distributed throughout the cell. Moreover, an in vitro enzyme activity assay indicated that the recombinant RcUGD3 protein catalyzed UDP-Glc to produce UDP-GlcA as shown by HPLC. Taken together, our results suggested that RcUGD3 protein is responsible for UDP-Glc degradation and probably plays a regulatory role in gallotannin biosynthesis in the Chinese gallnut. Conclusions: This study lays a foundation for further elucidating the function and expression regulation mechanism of the RcUGD gene family and provides new insights for the super-accumulation mechanisms of gallotannins in Chinese gallnuts. Full article

Plagiodera versicolora (Coleoptera: Chrysomelidae), the willow leaf beetle, is a leaf-eating pest that generally occurs on salicaceous trees. However, there is a blank of identification and phylogenetic relationship of the detoxification genes in P. versicolora. Here, we identified four detoxification gene families (glutathione S-transferases: GSTs, UDP-glycosyltransferases: UGTs, cytochrome P450 monooxygenases: CYPs and carboxylesterases: COEs) from the adult antennal transcriptome data. In all, 146 candidate detoxification genes including 22 GSTs, 20 UGTs, 60 CYPs, and 44 COEs were identified. We used quantitative real-time PCR technology to explore the tissue expression patterns of 12 PvGSTs in P. versicolora. The results showed that 7 PvGSTs have significantly high expression in antennae, indicating these PvGSTs may play an important role in degrade and/or inactivate the sex pheromones and host volatiles. The identification and phylogenetics of the detoxification genes in P. versicolora extended the database in Coleoptera and contributed to the subsequent in-depth research for function about detoxification genes. Full article

FAR1/FHY3 transcription factors are key regulators of plant growth and development, but their identification and functions in strawberries (Fragaria × ananassa) remain largely unexplored. In this study, 47 FaFAR1/FHY3 genes in cultivated strawberries were systematically identified, which were categorized into six subfamilies and randomly distributed across 15 chromosomes, with segmental duplication as the main driver of the expansion of this gene family. Integration of phylogenetic relationships, gene structure, and conserved motif composition uncovered distinct divergences among the subfamilies. A cis-acting element analysis of promoters and gene expression profiles showed that these genes responded to various abiotic and biotic stresses, phytohormones, and far-red light signals, with FaFAR1-7 and FaFAR1-44 strongly responding to multiple stresses, including temperature, drought, and pathogen infection. Additionally, FaFAR1-12 and FaFAR1-18 exhibited positive correlations with anthocyanin accumulation and the expression of key anthocyanin biosynthesis genes during fruit development. Dual-luciferase reporter assays further confirmed that FaFAR1-12 and FaFAR1-18 significantly activated the promoters of key structural genes related to anthocyanin biosynthesis, indicating that these two TFs exert vital regulatory functions in anthocyanin accumulation during strawberry fruit development. This study comprehensively identifies and characterizes the FaFAR1/FHY3 genes in cultivated strawberries, laying a foundation for their functional analysis and for screening out the key regulatory genes for strawberry fruit quality improvement. Full article

Background: Anthocyanin biosynthesis is tightly controlled by MYB transcription factors, yet the role of repressors, particularly those in the DIVARICATA-like (DIV) subfamily, remains poorly characterized. Methods: A genome-wide identification of MYB family members was performed in the mulberry (Morus atropurpurea) genome using a hidden Markov model and BLAST-based searches. Putative MYB genes were phylogenetically classified, and their expression profiles were analyzed across three fruit developmental stages. A DIV-like R2R3-MYB candidate, MaDIV, was functionally characterized via subcellular localization, quantitative real-time PCR, and heterologous overexpression in tobacco. Results: A total of 145 MaMYB genes were identified and classified into 31 distinct subfamilies. MaDIV expression showed a progressive decline during fruit ripening, which significantly correlated with increasing anthocyanin accumulation. Heterologous overexpression of MaDIV in tobacco led to a 42% reduction in floral anthocyanin content compared with wild-type plants. Concomitantly, the expression of the key anthocyanin biosynthetic gene NtDFR was strongly suppressed, whereas the flavonol synthase gene NtFLS1 was significantly upregulated. Conclusions: These findings point to a possible involvement of MaDIV in the regulation of anthocyanin biosynthesis and provide preliminary evidence for the functional diversification of the DIV-like MYB subfamily in plants. The results contribute to a better understanding of the transcriptional control of fruit pigmentation in mulberry and related species. Full article

Auxin response factors (ARFs) are pivotal regulators mediating plant growth, development, and abiotic stress responses, especially during seed germination under stressful conditions. However, the ARF gene family has not been thoroughly studied or characterized in sesame. The identification and characterization of ARF family members in the sesame genome were analyzed by bioinformatics methods, and the expression patterns of sesame ARF genes were assessed by quantitative real-time PCR. In this study, a total of 23 ARF genes were identified in the sesame genome, distributed unevenly across 12 chromosomes. Additionally, 15 segmental duplication events were detected. Phylogenetic analysis classified the SiARF genes into four subfamilies, with members within each subgroup sharing conserved structural features and motif compositions. Promoter analysis revealed multiple cis-acting elements associated with plant growth, phytohormone responses, and stress responses. Expression profiling demonstrated distinct tissue-specific expression patterns among the SiARF genes. Notably, SiARF5 and SiARF15 showed predominant expression in seeds 5 days after pollination, whereas SiARF14 exhibited broad expression in roots, stems, leaves, and seeds germinated for 24 h. QRT-PCR analysis identified eight SiARF genes exhibiting biphasic expression patterns during seed germination under abiotic stresses, characterized by initial downregulation and subsequent upregulation. Among them, SiARF11 showed significant induction under all three stress conditions, while SiARF9 was specifically upregulated under salt stress, suggesting their critical roles in stress response regulation. These findings provide a foundation for further investigation into Auxin-mediated responses to abiotic stress during seed germination in sesame. Full article

JAZ (Jasmonate ZIM-Domain) proteins are key negative regulators of the jasmonic acid (JA) signaling pathway and are involved in various plant growth, development, and stress regulation. However, the functions of the JAZ gene family in Camellia nitidissima remain poorly understood. Here, ten CnJAZ genes were identified at the genome-wide level, encoding 134–398 amino acids and unevenly distributed across eight chromosomes. All CnJAZs were predicted to localize to the nucleus. Based on phylogenetic and structural analyses, the ten CnJAZs were classified into five subfamilies, with members of the same subfamily sharing similar exon–intron structures. Collinearity analysis with Arabidopsis thaliana and Malus domestica suggests that the JAZ gene family shares a common ancestor. Promoter analysis revealed cis-acting elements responsive to light, methyl jasmonate (MeJA), and anaerobic stress. Transcriptome profiling showed that most CnJAZs exhibit tissue- and development-specific expression, particularly during flower development and organ formation. RT-qPCR confirmed that MeJA and gibberellin (GA₃) significantly induced the expression of CnJAZ, whereas ethylene (ETH) treatment up-regulated CnJAZ3 and CnJAZ5 by 80-fold after three hours. These findings highlight their important roles in growth, development, and hormonal regulation in C. nitidissima, laying a foundation for functional studies. Full article

Polygalacturonase (PG) is a key enzyme in cell wall metabolism and fruit ripening. Atemoya (Annona cherimola Mill. × A. squamosa L.) is a high-value tropical fruit that undergoes rapid postharvest softening at room temperature. However, the role of the atemoya PG gene family in this process remains unknown. This study determined that storing atemoya at 28 °C significantly reduced fruit firmness and the total pectin content but increased water-soluble pectin (WSP) and PG activity compared to storage at 15 °C. Genome-wide identification of the AaPG gene family in atemoya revealed that 40 AaPG genes were unevenly distributed across seven chromosomes. Nineteen genes were located within six tandem duplication clusters. AaPG proteins exhibited clade-specific differences: Clades B-E contained the polysaccharide lyase family 6 (PL-6) superfamily domain, while Clade A harbored the Aspergillus niger polygalacturonase 1 (Pgu1) domain and lacked several conserved motifs. Expression profiling and reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed that AaPG19, AaPG21, AaPG23 and AaPG24 were specifically induced at 28 °C. Subcellular localization confirmed that these four proteins were located on the plasma membrane. These findings provide insights into the evolution and temperature-dependent regulation of the AaPG family, identifying candidate genes responsible for the rapid softening of atemoya fruit. Full article

Potato (Solanum tuberosum L.) is the world’s fourth-largest staple crop. Alkaline salt stress is a major abiotic stress factor that severely limits the growth, yield, and quality of potatoes; however, little is known about the molecular basis of potatoes’ response to alkaline salt stress or the stress-alleviation mechanism mediated by 24-epibrassinoside. In this study, we conducted a genome-wide identification of the potato miR482 family and analyzed its response patterns under alkaline salt stress and 24-epibrassinoside-mediated stress relief. We identified a total of 9 mature stu-miR482 sequences and 5 precursor sequences; all precursors form typical stable hairpin structures and exhibit high evolutionary conservation among Solanaceae plants. Promoter analysis revealed multiple cis-acting elements in the promoter region associated with light signaling, plant hormones, and stress signaling. A total of 64 potential target genes were predicted, encompassing transcription factors, disease resistance, and signal transduction-related genes, forming a complex regulatory network. Phenotypic analysis confirmed that EBR significantly alleviates the growth inhibition in potatoes induced by alkaline salt stress. qRT-PCR analysis indicated that stu-miR482a-5p is the primary stress-responsive member in leaves; stu-miR482d-3p/5p exhibited the strongest regulatory response to EBR in roots; in potato stolons, all members of the miR482 family were significantly upregulated under alkaline salt stress, with stu-miR482d-5p showing extremely significant upregulation across all treatment groups. In summary, this study represents the first systematic characterization of the potato miR482 family, revealing its tissue differential functions in alkaline salt stress and EBR-mediated stress relief. Full article