Search Results (528)

Background/Objectives: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (Setaria italica) lacks comprehensive characterization of its LEA gene family. This study aimed to comprehensively identify SiLEA genes in foxtail millet and elucidate their functional roles and tissue-specific expression patterns. Methods: Genome-wide identification of SiLEA genes was conducted, followed by phylogenetic reconstruction, cis-acting element analysis of promoters, synteny analysis, and expression profiling. Results: Ninety-four SiLEA genes were identified and classified into nine structurally distinct subfamilies, which are unevenly distributed across all nine chromosomes. Phylogenetic analysis showed closer clustering of SiLEA genes with sorghum and rice orthologs than with Arabidopsis thaliana AtLEA genes. Synteny analysis indicated the LEA gene family expansion through tandem and segmental duplication. Promoter cis-element analysis linked SiLEA genes to plant growth regulation, stress responses, and hormone signaling. Transcriptome analysis revealed tissue-specific expression patterns among SiLEA members, while RT-qPCR verified ABA-induced transcriptional regulation of SiLEA genes. Conclusions: This study identified 94 SiLEA genes grouped into nine subfamilies with distinct spatial expression profiles. ABA treatment notably upregulated SiASR-2, SiASR-5, and SiASR-6 in both shoots and roots. Full article

Late-spring frost events severely damage low-chill peach blossoms, causing significant yield losses. Although 5-aminolevulinic acid (ALA) enhances cold tolerance through the PpC3H37-PpWRKY18 module, the regulatory mechanism of ALA on PpC3H37 remains to be elucidated. Using yeast one-hybrid screening with the PpC3H37 promoter as bait, we identified PpDof9 as a key interacting transcription factor. A genome-wide analysis revealed 25 PpDof genes in peaches (Prunus persica). These genes exhibited variable physicochemical properties, with most proteins predicted as nuclear-localized. Subcellular localization experiments in tobacco revealed that PpDof9 was localized to the nucleus, consistent with predictions. A synteny analysis indicated nine segmental duplication pairs and tandem duplications on chromosomes 5 and 6, suggesting duplication events drove family expansion. A conserved motif analysis confirmed universal presence of the Dof domain (Motif 1). Promoter cis-element screening identified low-temperature responsive (LTR) elements in 12 PpDofs, including PpDof1, PpDof8, PpDof9, and PpDof25. The quantitative real-time PCR (qRT-PCR) results showed that PpDof1, PpDof8, PpDof9, PpDof15, PpDof16, and PpDof25 were significantly upregulated under low-temperature stress, and this upregulation was further enhanced by ALA pretreatment. Our findings demonstrate ALA-mediated modulation of specific PpDof TFs in cold response and provide candidates (PpDof1, PpDof9, PpDof8, PpDof25) for enhancing floral frost tolerance in peaches. Full article

The red plant phenotype of R1 cotton is a genetic marker produced by light-induced anthocyanin accumulation. GhPAP1D controls this trait. There are two 228 bp tandem repeats upstream of GhPAP1D in R1 cotton. In this study, GUS staining assays in transgenic Arabidopsis thaliana (L.) Heynh. demonstrated that tandem repeats in the GhPAP1D promoter-enhanced transcriptional activity. GhPAP1D is a homolog of A. thaliana AtPAP1. AtPAP1’s expression is regulated by photomorphogenesis-related transcription factors such as AtHY5 and AtBBXs. We identified the homologs of A. thaliana AtHY5, AtBBX21, and AtBBX24 in R1 cotton, designated as GhHY5, GhBBX21, and GhBBX24, respectively. Y1H assays confirmed that GhHY5, GhBBX21, and GhBBX24 each bound to the GhPAP1D promoter. Dual-luciferase reporter assays revealed that GhHY5 weakly activated the promoter activity of GhPAP1D. Heterologous expression assays in A. thaliana indicated that GhBBX21 promoted anthocyanin accumulation, whereas GhBBX24 had the opposite effect. Dual-luciferase assays showed GhBBX21 activated GhPAP1D transcription, while GhBBX24 repressed it. Further study indicated that GhHY5 did not enhance GhBBX21-mediated transcriptional activation of GhPAP1D but alleviates GhBBX24-induced repression. Together, our results demonstrate that GhBBX21 and GhBBX24 antagonistically regulate anthocyanin accumulation in R1 cotton under GhHY5 mediation, providing insights into light-responsive anthocyanin biosynthesis in cotton. Full article

Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the RBCS gene family in C3 and C4 grasses to identify genetic targets for improved crop photosynthesis. Triticeae/Aveneae phylogeny groups exhibited a syntenic tandem duplication array averaging 326.1 Kbp on ancestral chromosomes 2 and 3, with additional copies on other chromosomes. Promoter analysis revealed a paired I-box element promoter arrangement in chromosome 5 RBCS of H. vulgare, S. cereale, and A. tauschii. The I-box pair was associated with significantly enhanced expression, suggesting functional adaptation of specific RBCS gene copies in Triticaeae. H. vulgare-derived pan-transcriptome data showed that RBCS expression was 50.32% and 28.44% higher in winter-type accessions compared to spring types for coleoptile (p < 0.05) and shoot, respectively (p < 0.01). Molecular dynamics simulations of a mutant H. vulgare Rubisco carrying a C4-like amino acid substitution (G59C) in RBCS significantly enhanced the stability of the Rubisco complex. Given the known structural efficiency of C4 Rubisco complexes, G59C could serve as an engineering target for enhanced RBCS in economically crucial crop species which, in comparison, possess less efficient Rubisco complexes. Full article

The cytokinin response regulator (ARR) gene is essential for cytokinin signal transduction, which plays a crucial role in plant growth and development. However, the functional mechanism of ARR genes in cotton leaf abscission remains incompletely understood. In this study, a total of 86 ARR genes were identified within the genome of Gossypium hirsutum. These genes were categorized into four distinct groups based on their phylogenetic characteristics, supported by analyses of gene structures and conserved protein motifs. The GhARR genes exhibited an uneven distribution across 25 chromosomes, with three pairs of tandem duplication events observed. Both segmental and tandem duplication events significantly contributed to the expansion of the ARR gene family. Furthermore, numerous putative cis-elements were identified in the promoter regions, with hormone and stress-related elements being common among all 86 GhARRs. Transcriptome expression profiling screening results demonstrated that GhARRs may play a mediating role in cotton’s response to TDZ (thidiazuron). The functional validation of GhARR16, GhARR43, and GhARR85 using virus-induced gene silencing (VIGS) technology demonstrated that the silencing of these genes led to pronounced leaf wilting and chlorosis in plants, accompanied by a substantial decrease in petiole fracture force. Overall, our study represents a comprehensive analysis of the G. hirsutum ARR gene family, revealing their potential roles in leaf abscission regulation. Full article

Higher education has long been subject to feminist critique, contesting traditional practices, with calls for transformative pedagogies that empower marginalised students, address social injustices and promote gender equality. Despite this, most classrooms in Western European universities remain largely unchanged, with educators facing the difficulty of imagining and/or enacting decolonial futures within their curricula. However, some progress has been made, particularly the inclusion of transnational scholarship in syllabi and a turn to transformative pedagogies, which allow for alternative ways of interdisciplinary knowing to enter academia. In this paper, we examine this coming together of approaches which promote dialogue and personal reflection to restructure discussions on equality, gender and knowledge production in the ‘classroom’. Using a creative critical account of feminist ethnography conducted at a Western European university, we present and discuss two illustrative vignettes about cultural mapping and critical fabulation, considering how dissonant voices have challenged Western concepts, exemplifying transformative pedagogy working in tandem with transnational thought. Key insights from the study identify approaches for facilitation of more open and richer discussions to reshape staff and student perspectives of gender, equality and knowledge production. Full article

UDP-glycosyltransferases (UGTs) play essential roles in various biological processes, such as phytohormone homeostasis, abiotic stress adaptation, and secondary metabolite biosynthesis. Populus euphratica is a model species for investigating stress adaptation; however, the PeUGT gene family has yet to be systematically characterized. Here, we identified 134 UGT genes in P. euphratica. Phylogenetic analysis classified these genes into 16 major groups (A–P), and UGT genes within the same groups showed similar structural characteristics. Tandem duplication events were identified as the predominant mechanism driving the expansion of the PeUGT family. Cis-acting element analysis revealed an enrichment of motifs associated with developmental regulation, light response, phytohormone signaling, and abiotic stress in the promoters of PeUGT genes. Expression profiling demonstrated spatiotemporal regulation of the PeUGT genes under drought stress. Among them, PeUGT110 was significantly induced by PEG treatment in the leaf, root, and stem tissues of P. euphratica. Overexpression of PeUGT110 enhanced drought tolerance in transgenic Arabidopsis. Furthermore, the PeUGT110-OE lines exhibited reduced malonaldehyde accumulation, elevated proline content, higher superoxide dismutase activity, and upregulated expression of stress-related genes under drought stress. The results demonstrated that PeUGT110 plays a critical role in plant drought resistance. These findings establish a foundation for elucidating the function of PeUGT genes. Full article

The germin-like protein (GLP) family plays vital roles for plant growth, stress adaptation, and defense; however, its evolutionary dynamics and functional diversity in halophytes remain poorly characterized. Here, we present the genome-wide analysis of the GLP family in the halophytic forage alkaligrass (Puccinellia tenuiflora), which identified 54 PutGLPs with a significant expansion compared to other plant species. Phylogenetic analysis revealed monocot-specific clustering, with 41.5% of PutGLPs densely localized to chromosome 7, suggesting tandem duplication as a key driver of family expansion. Collinearity analysis confirmed evolutionary conservation with monocot GLPs. Integrated gene structure and motif analysis revealed conserved cupin domains (BoxB and BoxC). Promoter cis-acting elements analysis revealed stress-responsive architectures dominated by ABRE, STRE, and G-box motifs. Tissue-/organ-specific expression profiling identified root- and flower-enriched PutGLPs, implying specialized roles in stress adaptation. Dynamic expression patterns under salt-dominated stresses revealed distinct regulatory pathways governing ionic and alkaline stress responses. Functional characterization of PutGLP37 demonstrated its cell wall localization, dual superoxide dismutase (SOD) and oxalate oxidase (OXO) enzymatic activities, and salt stress tolerance in Escherichia coli, yeast (Saccharomyces cerevisiae INVSc1), and transgenic Arabidopsis. This study provides critical insights into the evolutionary innovation and stress adaptive roles of GLPs in halophytes. Full article

Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first complete assembly and comprehensive analysis of the P. ludlowii mitochondrial genome. Most remarkably, we discovered that the P. ludlowii mitogenome exhibits an atypical dual-circular structure, representing the first documented occurrence of this architectural feature within the genus Paeonia. The assembled genome spans 314,371 bp and encodes 42 tRNA genes, 3 rRNA genes, and 31 protein-coding genes, with a pronounced adenine–thymine bias. This multipartite genome structure is characterized by abundant repetitive elements (112 functionally annotated SSRs, 33 tandem repeats, and 945 dispersed repeats), which potentially drive genome rearrangements and facilitate adaptive evolution. Analyses of codon usage bias and nucleotide diversity revealed highly conserved gene expression regulation with limited variability. Phylogenetic reconstruction confirms that P. ludlowii, P. suffruticosa, and P. lactiflora form a monophyletic clade, reflecting close evolutionary relationships, while extensive syntenic collinearity with other Paeonia species underscores mitochondrial genome conservation at the genus level. Extensive inter-organellar gene transfer events, particularly from chloroplast to mitochondrion, suggest that such DNA exchanges enhance genetic diversity and promote environmental adaptation. The discovery of the dual-circular architecture provides novel insights into plant mitochondrial genome evolution and structural plasticity. This study elucidates the unique structural characteristics of the P. ludlowii mitochondrial genome and establishes a crucial genetic foundation for developing targeted conservation strategies and facilitating molecular-assisted breeding programs for this endangered species. Full article

Caffeic acid-O-methyltransferase (COMT) is a key enzyme in lignin synthesis and secondary metabolism in plants, and it participates in the regulation of plant growth and development as well as plants’ stress response. To further investigate the function of COMT in grapevine, a total of 124 COMT family genes were identified from three Vitis species in this study, namely Pinot noir (Vitis vinifera L.), Vitis amurensis, and Vitis riparia. The amino acid sequence encoded by these genes ranged from 55 to 1422 aa, and their molecular mass ranged from 6640.82 to 77,034.43 Da. Subcellular localization prediction inferred that they were mainly located in the plasma membrane and cytoplasm. The prediction of secondary structures showed that α-helix and irregular coiled-coil were primary structural elements. These genes were unevenly distributed across 10 different chromosomes, respectively. Phylogenetic tree analysis of the amino acid sequences of VvCOMT, VaCOMT, VrCOMT, and AtCOMT proteins showed that they were closely related and were divided into four subgroups. The motif distribution was similar among the cluster genes, and the gene sequence was notably conserved. The 124 members of the COMT gene family possessed a variable number of exons, ranging from 2 to 13. The promoter region of all of these COMTs genes contained multiple cis-acting elements related to hormones (e.g., ABA, IAA, MeJA, GA, and SA), growth and development (e.g., endosperm, circadian, meristem, light response), and various stress responses (e.g., drought, low temperature, wounding, anaerobic, defense, and stress). The intraspecies collinearity analysis suggested that there were one pair, three pairs, and six pairs of collinear genes in Va, Pinot noir, and Vr, respectively, and that tandem duplication contributed more to the expansion of these gene family members. In addition, interspecific collinearity revealed that the VvCOMTs had the strongest homology with the VaCOMTs, followed by the VrCOMTs, and the weakest homology with the AtCOMTs. The expression patterns of different tissues and organs at different developmental stages indicated that the VvCOMT genes had obvious tissue expression specificity. The majority of VvCOMT genes were only expressed at higher levels in certain tissues. Furthermore, we screened 13 VvCOMT genes to conduct qRT-PCR verification according to the transcriptome data of VvCOMTs under abiotic stresses (NaCl, PEG, and cold). The results confirmed that these genes were involved in the responses to NaCl, PEG, and cold stress. This study lays a foundation for the exploration of the function of the COMT genes, and is of great importance for the genetic improvement of abiotic stress resistance in grapes. Full article

The heavy metal-associated (HMA) domain-harboring proteins constitute critical players involved in the transport of various metal ions in plants, and are associated with development and stress responses. Herein, a total of 243 TaHMA genes were identified in the bread wheat genome, each of which had a characteristic molecular profile and a distinct chromosomal localization. The TaHMA proteins were distributed in five clades in phylogeny, which differed with respect to the distribution of the key HMA domain. Sub-cellular localization was variable for the TaHMA proteins. Gene structure analysis yielded similar results when compared with the orthologous counterparts. Cis-regulatory element analysis produced a range of promoter elements, suggesting their diverse biological roles. Gene duplication analysis revealed a crucial role played by tandem and segmental duplication events in the expansion of TaHMA genes. Synteny analysis highlighted the evolutionary relatedness of TaHMA genes with those derived from Arabidopsis and rice. Expression analysis provided crucial information about the role of TaHMAs in mediating vital responses in the plant body, including the development of tissues and the regulation of various abiotic stress conditions. Overall, the study provides significant cues and evidence to functionally annotate and characterize the differentially expressed TaHMAs in order to validate their role. Full article

MIKC-type MADS-box transcription factors constitute one of the largest gene families in plants, playing pivotal roles in regulating plant growth and development, hormone signaling transduction, and responses to biotic and abiotic stresses. However, there have been no reports on the systematic identification and characterization of MIKC-type MADS-box proteins in walnuts. In this study, we identified 52 JrMADS genes in the walnut genome and transcriptome, and categorized them into 14 subfamilies through structural domain and phylogenetic tree analysis. It was found that these genes were unevenly distributed across 16 chromosomes. Within the MIKC-type MADS-box gene family, we identified three pairs of tandem-duplicated genes and 40 pairs of segmental duplicated genes, indicating that segmental duplication was the primary mechanism of gene amplification in walnut. Ka/Ks analysis showed that the family genes have undergone purifying selection during evolutionary processes. The promoter was predicted to contain cis-acting elements related to growth, development, plant hormones, and stress response. Expression profile analysis showed that JrMADS genes have different expression patterns in various tissues and developmental stages of male and female flower buds. Notably, an ancient clade of TM8 (JrMADS43) genes was found, which is absent in Arabidopsis but present in other flowering plants. Another gene, TM6 gene (JrMADS4), belongs to the AP3 subfamily and is a clade that has diverged from tomatoes. Through qPCR analysis, we verified the differential expression of JrMADS genes at different developmental stages (MB-1/2/3 and FB-1/2/3), with JrMADS5, JrMADS8, JrMADS14, JrMADS24, JrMADS40, JrMADS46, JrMADS47, JrGA3ox1, and JrGA3ox3 showing significantly higher expression in male than in female flower buds. In summary, our results provide valuable information for further biological functions research on MIKC-type MADS-box genes in walnut, such as flower organ development, and lays a solid foundation for future studies. Full article

Background: Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) significantly enhance the median survival of patients with lung adenocarcinoma (ADC) that harbor EGFR-sensitive mutations. However, most patients inevitably experience tumor relapse owing to drug resistance. We aimed to identify potential serum biomarkers for predicting post-EGFR-TKI treatment relapse in patients with advanced-stage lung ADC. Methods: Among 27 patients, including 6 and 21 with early and late relapse, respectively, differentially expressed proteins between patients with early and late relapses were identified using liquid chromatography and tandem mass spectrometry and subsequently validated using Western blotting. Predictive ability was assessed using the receiver operating characteristic curve and area under the curve (AUC) analysis. The association between the clinical variables and treatment response was evaluated using the chi-square test. Results: The serum expression levels of the translocated promoter region (TPR), junction plakoglobin (JUP), and fibrinogen alpha chain (FGA) were significantly higher in patients with late rather than early relapse. The findings indicated that TPR and FGA exhibited good diagnostic performance, with AUCs of 0.946 (p = 0.002; 95% confidence interval [CI], 0.84–1.05) and 0.809 (p = 0.034; 95% CI, 0.65–0.97), respectively. Conclusions: Our results suggest that the TPR and FGA levels are potential predictors of post-EGFR-TKI treatment relapse. Full article

Light-harvesting chlorophyll a/b-binding (Lhc) proteins are integral membrane proteins that bind to pigment molecules, playing a critical role in photosynthetic processes, including light energy harvesting and transfer. To investigate the role of the Lhc gene family in cucumber (Cucumis sativus L), genome-wide identification of CsLhc gene family members and analysis of their regulatory networks were carried out using bioinformation and molecular biology research methods at Anhui Science and Technology University. The results indicated that the Lhc family consisted of 21 members, being categorized into five subfamilies: Lhca, Lhcb, CP24, CP26, and CP29. The gene structure and motifs within each subfamily are generally conserved. CsLhcs are distributed on seven chromosomes, including one pair of tandem duplicates and two pairs of segmental duplicates. Six CsLhcs exhibit eight linear relationships with seven AtLhcs, and one CsLhc shows a syntenic relationship with one OsLhc. Analysis of the cis-acting elements in CsLhc promoters revealed their potential involvement in stress responses. Transcriptome data indicated that CsLhcs are minimally expressed in male flowers and roots, but highly expressed in other organs. Analysis of stress response processes revealed that all Lhc genes participate in at least one stress response. Five Lhc genes were confirmed to appear to have expression change using qPCR analysis under high temperature and salt stress. Particularly, under downy mildew, root-knot nematode stresses, and blight stress, up-regulated Lhc genes were the most abundant ones, indicating that the Lhc family acts as a significant role in the growth and development of cucumber. These results provide valuable insights for further understanding the characteristics of the CsLhc family and analyzing the function of the Lhc family in cucumber resistance to biotic/abiotic stresses and in molecular breeding. Full article

The Cerasus humilis, a perennial shrub belonging to the Cerasus genus, is native to China and holds significant ecological and economic importance. Growth regulation factors (GRF) are a family of transcription factors (TF) that play a key role in plant growth and development. This research entailed an in-depth examination of the GRF family in C. humilis, exploring its significance in the evolution of C. humilis. Twelve GRF genes were identified in the C. humilis genome. Named separately as ChGRF1-Chumilis15987.1, ChGRF2-Chumilis25207.1, ChGRF3-Chumilis26233.1, ChGRF4-Chumilis08578.3, ChGRF5-Chumilis18808.1, ChGRF6-Chumilis12052.1, ChGRF7-Chumilis10417.1, ChGRF8-Chumilis01608.1, ChGRF9-Chumilis14057.1, ChGRF10-Chumilis12169.1, ChGRF11-Chumilis14952.1, and ChGRF12-Chumilis07534.1. Phylogenetic analysis divided twelve GRF genes into five subfamilies. The gene structure, pattern, and cis-regulatory components of the GRF gene family were analyzed. In addition, according to collinearity analysis, there are six collinearity with Arabidopsis, twelve collinearity with Malus pumila, eight collinearity with Vitis vinifera, and three collinearity with Oryza sativa. Intraspecific collinearity analysis revealed the presence of three pairs of tandem repeat genes in the dwarf cherry genome. Identifying cis-acting elements revealed the prominent presence of gibberellin reaction elements, which are widely distributed in the promoter region. Cluster heatmap analysis showed that ChGRF2 had the highest expression levels in fruits and stems. ChGRF3 is highly expressed in red fruits of different colors, while ChGRF6 and ChGRF12 are highly expressed in yellow fruits. This study mainly focused on dwarf cherries treated with gibberellin. As the treatment time increased, the ChGRF gene showed different expression levels. ChGRF2, ChGRF3, ChGRF6, and ChGRF12 were up-regulated under gibberellin treatment. These genes all contain hormone-responsive cis-acting elements, indicating tht the ChGRF gene family plays a vital role under gibberellin treatment in C. humilis. The results laid the foundation for further research on the biological functions of the GRF genes in C. humilis. Full article