Search Results (2,558)

Trifolium repens L. (white clover) is a widely distributed perennial legume, which is regarded as one of the most important forages for its high protein content and excellent palatability. Low temperature limits the distribution and productivity of white clover, thereby reducing its economic returns. WRKY transcription factors are key regulators in stress defense and are involved in multiple abiotic stress responses in plants. In this study, a cold inducible gene named TrWRKY41 was cloned from white clover. The TrWRKY41 protein is predominantly localized in the nucleus and functions as a hydrophilic, acidic protein. Under cold stress, the overexpression plants had significantly higher chlorophyll (CHL) and proline (Pro) contents, significantly increased activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), and malondialdehyde (MDA) content significantly decreased. Compared to wild-type Arabidopsis thaliana, TrWRKY41-overexpressing plants exhibited better cold tolerance. In addition, target genes downstream of the TrWRKY41 transcription factor were predicted utilizing BLAST alignment and AlphaFold2 (version 0.2.0) software, the expression of six genes, including AtCOR47, AtCOR6.6, and AtABI5, was significantly up-regulated under cold stress. It suggests that TrWRKY41 may enhance cold tolerance in Arabidopsis by activating the ICE-CBF-COR cascade. This study provides candidate genes for research on enhancing the cold tolerance of white clover. Full article

Mitogen-Activated Protein Kinases (MAPKs) play crucial roles in plant stress signaling, but the mechanisms of MAPK genes in Portulaca oleracea remain functionally uncharacterized. In this study, transcriptomic screening of P. oleracea under salt stress identified PoMPK3 as a candidate gene, showing significant root-specific upregulation. Phylogenetic analysis classified it as a Group A MAPK protein, and subcellular localization confirmed its membrane association. Heterologous expression of PoMPK3 in Arabidopsis thaliana significantly enhanced salt tolerance, as evidenced by improved seed germination rates, longer primary roots, increased biomass, and reduced stress symptoms. Mechanistically, PoMPK3 expression activated ABA signaling, leading to increased ABA levels and upregulation of AtNCED3, AtPYR1, and AtABF3. Furthermore, it strengthened the antioxidant defense, as evidenced by elevated antioxidant enzyme activity, leading to a reduction in oxidative stress. The transgenic lines also demonstrated enhanced osmotic adjustment through osmolytes accumulation and ionic homeostasis, evidenced by tissue-specific Na⁺/K⁺ ratios (low in shoots, high in roots) resulting from the concerted upregulation of AtSOS1, AtNHX1, and AtHKT1. In addition, gene co-expression network analysis and molecular docking predicted phosphorylation of WRKY transcription factors, suggesting a novel mechanism for transcriptome reprogramming. Collectively, our findings not only advance the understanding of salt tolerance mechanisms in purslane but also identify PoMPK3 as a key genetic determinant, thereby laying the foundation for its use in breeding programs aimed at enhancing salt stress resilience in crops. Full article

Basic leucine zipper (bZIP) transcription factors play pivotal roles in plant secondary metabolism, influencing the production of bioactive compounds that determine the medicinal value of plants. Despite their significance, a comprehensive genomic overview of bZIPs in non-model medicinal species remains limited. Here, we present the first genome-wide identification and characterization of the bZIP family in Lycium ruthenicum Murr. (black wolfberry), revealing 63 members grouped into 13 subfamilies. These genes showed conserved bZIP domains, distinct exon–intron architectures, and promoter cis-elements related to light, hormones and stress responses. Family expansion occurred through tandem (LrbZIP6-LrbZIP9 cluster) and segmental duplications under purifying selection (Ka/Ks < 1). Collinearity analysis revealed closer relationships with Solanaceae species than Arabidopsis thaliana, with LrbZIP10 and LrbZIP11 as conserved orthologs. Expression profiling identified tissue-specific patterns: LrbZIP17 showed broad expression while LrbZIP14 was fruit-specific. qRT-PCR confirmed floral-preferential (LrbZIP1, LrbZIP10, LrbZIP15, LrbZIP17, LrbZIP50) and root-specific (LrbZIP54, LrbZIP55) expression. The co-occurrence of light/hormone-responsive elements and high LrbZIP expression in anthocyanin-rich tissues suggests their regulatory roles in bioactive compound biosynthesis. This study provides foundational genomic resources for understanding L. ruthenicum bZIP evolution and identifies candidate genes for molecular breeding to enhance medicinal compound production. Full article

Zinc (Zn) is an essential trace element that plays a crucial role in plant growth and development, but excessive Zn can be stressful or even toxic to plants. The GLTP superfamily is critical for lipid metabolism and membrane stability maintenance, yet its function in plant Zn tolerance remains unclear. In this study, zinc stress treatment experiments were performed using transgenic apple calli, apple seedlings, Arabidopsis thaliana, and Solanum lycopersicum. Under Zn treatment, compared with the wild type (WT), the apple seedlings of the MbACD11 transgenic line exhibited significantly higher plant height and fresh weight, with increases of 5.87% and 93.21% respectively. Meanwhile, their MDA level, relative electrical conductivity, and accumulations of H₂O₂ and O₂⁻ were all significantly reduced, with decreases of 20.47%, 35.47%, 31.50%, and 36.78% respectively. Consistently, these data showed the same trend in calli, Arabidopsis thaliana, and tomato. These results demonstrated that the overexpression of MbACD11 significantly enhanced Zn tolerance in transgenic plants, and also verified that the function of this gene may be conserved across different species. In summary, this study establishes a molecular framework and theoretical basis for improving plant tolerance to Zn stress and paves the way for future mechanistic investigations. Full article

RNA methylation, particularly N6-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C), functions as a pivotal post-transcriptional regulatory mechanism and plays a central role in plant growth, development, and stress responses. This review provides a systematic summary of recent advances in RNA methylation research in cucurbit crops. To date, high-throughput technologies such as MeRIP-seq and nanopore direct RNA sequencing have enabled the preliminary construction of RNA methylation landscapes in cucurbit species, revealing their potential regulatory roles in key agronomic traits, including fruit development, responses to biotic and abiotic stresses, and disease resistance. Nevertheless, this field remains in its early stages for cucurbit crops and faces several major challenges: First, mechanistic understanding is still limited, with insufficient knowledge regarding the composition and biological functions of the core protein families involved in methylation dynamics—namely, “writers,” “erasers,” and “readers.” Second, functional validation remains inadequate, as direct evidence linking specific RNA methylation events to downstream gene regulation and phenotypic outcomes is largely lacking. Third, resources are scarce; compared to model species such as Arabidopsis thaliana and rice, cucurbit crops possess limited species-specific genetic data and genetic engineering tools (e.g., CRISPR/Cas9-based gene editing systems), which significantly hampers comprehensive functional studies. To overcome these limitations, future research should prioritize the development and application of more sensitive detection methods, integrate multi-omics datasets—including transcriptomic and methylomic profiles—to reconstruct regulatory networks, and conduct rigorous functional assays to establish causal relationships between RNA methylation modifications and phenotypic variation. The ultimate objective is to fully elucidate the biological significance of RNA methylation in cucurbit plants and harness its potential for crop improvement through genetic and biotechnological approaches. Full article

Soil salinization significantly limits plant growth and agricultural productivity, with MYB transcription factors playing crucial roles in mediating plant responses to salt stress. In this study, a novel R2R3-MYB transcription factor gene, SlMYB306-like, was isolated from tomato. Phylogenetic comparison indicated that SlMYB306-like shared the highest sequence homology with potato StMYB306-like. Subcellular localization assays demonstrated nuclear localization of SlMYB306-like protein, while yeast transactivation assays confirmed its function as a transcriptional activator. Expression profiling showed that SlMYB306-like was inducible by NaCl and abscisic acid (ABA) treatments. In addition, functional characterization via the overexpression of SlMYB306-like in Arabidopsis thaliana revealed enhanced salt tolerance, evidenced by an increased maximum quantum efficiency of photosystem II (Fv/Fm) and proline levels alongside decreased accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) content under salt stress conditions. Furthermore, the overexpression of SlMYB306-like upregulated the expression of several stress-responsive genes, including AtSOD1, AtCAT1, AtEGY3, AtP5CS2, and AtRD29A. Collectively, these findings suggest that SlMYB306-like enhances salt tolerance by modulating ROS scavenging, osmotic adjustment, and ABA signaling pathways, thereby representing a promising candidate gene for the development of salt-tolerant crops. Full article

Leguminous plants are critical global crops for food security, animal feed, and ecological sustainability due to their ability to establish nitrogen-fixing symbioses with rhizobia and their high nutritional value. Autophagy, a highly conserved eukaryotic catabolic process, mediates the degradation and recycling of cytoplasmic components through the fusion of autophagosome with vacuole/lysosome and plays essential roles in plant growth, stress adaptation, and cellular homeostasis. This review systematically summarizes current knowledge of autophagy in both Arabidopsis and leguminous plants. We first outline the conserved molecular machinery of autophagy, focusing on core autophagy-related (ATG) genes in Arabidopsis and key legume species such as Glycine max, Arachis hypogaea, Pisum sativum, Cicer arietinum, and Medicago truncatula. Furthermore, the review dissects the intricate molecular regulatory networks controlling autophagy, with an emphasis on the roles of phytohormones, transcription factors, and epigenetic modifications. We then highlight the multifaceted physiological functions of autophagy in these plants. Additionally, a preliminary analysis of the ATG8 gene family in peanut indicates that its members may be involved in seed development, biological nitrogen fixation, and drought resistance. Finally, it highlights key unresolved challenges in legume autophagy research and proposes future research directions. This review aims to provide a comprehensive theoretical framework for understanding the unique regulatory mechanisms of autophagy in legumes and to provide insights for molecular breeding aimed at developing stress-resilient, high-yielding, and high-quality legume cultivars. Full article

Recent developments of Normalized Compressed Distance (NCD) matrices show potential to become a widely used method to develop phylogenetic trees among a group of organisms. However, such NCD matrices lack the biological and evolutionary context that is important to the development of phylogenetic trees. This study applied mathematical models of DNA evolution to NCD matrices with the goal of applying evolutionary context to improve the results of NCD methods and thus create better phylogenetic trees. Mammalian mitochondrial, Arabidopsis thaliana, and Tomato Solanum lycopersicum genomes were used in this study as benchmarks and underwent validation techniques to analyze whether the NCD matrix models were of better quality than their original NCD. The mathematical models applied were not sufficient in implementing a biological context towards NCD compression algorithms for phylogenetic trees, resulting in no successful improvement of them. However, this opens opportunities to explore ways to integrate biological context internally to NCD compression algorithms, rather than external methods of correcting NCD matrices after compression has been carried out. Full article

Backgrounds: Accurate annotation of open reading frames (ORFs) is fundamental for understanding gene function and post-transcriptional regulation. A critical but often overlooked aspect of transcriptome annotation is the selection of authentic translation start sites. Many genome annotation pipelines identify the longest possible ORF in alternatively spliced transcripts, using internal methionine codons as putative start sites. However, this computational approach ignores the biological reality that ribosomes select start codons based on sequence context, not ORF length. Methods: Here, we demonstrate that this practice leads to systematic misannotation of nonsense-mediated decay (NMD) targets in the Arabidopsis thaliana Araport11 reference transcriptome. Using TranSuite software to identify authentic start codons, we reanalyzed transcriptomic data from an NMD-deficient mutant. Results: We found that correct ORF annotation more than doubles the number of identifiable NMD targets with premature termination codons followed by downstream exon junctions, from 203 to 426 transcripts. Furthermore, we show that incorrect ORF annotations can lead to erroneous protein structure predictions, potentially introducing computational artefacts into protein databases. Conclusions: Our findings underscore the importance of biologically informed ORF annotation for accurate assessment of post-transcriptional regulation and proteome prediction, with implications for all eukaryotic genome annotation projects. Full article

Lignin constitutes a fundamental component of plant defense mechanisms against environmental stressors. 4-coumarate 3-hydroxylase (C3H) serves as a pivotal enzyme in lignin biosynthesis. However, its role in the halophyte Sesuvium portulacastrum remains uncharacterized. In this study, the SpC3H gene was cloned, and subsequent sequence alignment and phylogenetic analyses revealed the highest similarity (57.14%) with BvC3H from Beta vulgaris, exhibiting the closest evolutionary relationship with Beta vulgaris and Spinacia oleracea C3H protein. Quantitative real-time polymerase chain reaction demonstrated that SpC3H expression was markedly upregulated in both roots and leaves of S. portulacastrum under 800 mM NaCl treatment. Root expression peaked at 48 h (25.3-fold), whereas leaves displayed dual expression maxima at 12 h (7.9-fold) and 72 h (10.7-fold). Subcellular localization assays confirmed cytoplasmic distribution. Heterologous expression in Arabidopsis thaliana indicated that transgenic lines exhibited enhanced growth performance, higher fresh weight, and elevated lignin contents relative to wild-type plants under salt stress, accompanied by reduced reactive oxygen species (ROS) accumulation and lower relative electrical conductivity. Furthermore, activities of superoxide dismutase and peroxidase, together with expression of lignin biosynthesis-associated and antioxidant enzyme genes, were markedly elevated. Collectively, these findings establish that SpC3H confers salt tolerance by promoting lignin biosynthesis and activating antioxidant defenses to eliminate ROS, thereby providing a theoretical foundation for genetic improvement of plant salt tolerance. Full article

Soybean (Glycine max) is a vital oilseed and economic crop in China, often constrained by drought, salinity, and biotic stresses. In this study, we identified a soybean bZIP transcription factor, GmbZIP59, whose expression is upregulated by salt, drought, ethylene (ETH), methyl jasmonate (MeJA), and abscisic acid (ABA). Overexpression of GmbZIP59 in Arabidopsis (OE-13 and OE-20, two independent Arabidopsis transgenic lines) exhibited enhanced resistance to Sclerotinia sclerotiorum (S. sclerotiorum), improved tolerance to salt stress, and increased sensitivity to phytohormones. Overexpression of GmbZIP59 in rice (OE-1 and OE-2, two independent rice transgenic lines) improved tolerance to salt and drought stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that elevated expression of stress-related genes occurred in transgenic lines under adverse conditions. Furthermore, chromatin immunoprecipitation-qPCR (ChIP-qPCR) assays confirmed that GmbZIP59 directly binds to the promoters of ETH, MeJA, and ABA, responsive genes associated with stress responses. These findings demonstrate that GmbZIP59 acts as a positive regulator of biotic and abiotic stress tolerance in soybean. Full article

Russian dandelion (Taraxacum kok-saghyz Rodin, TKS) is a natural rubber (NR)-producing species whose roots contain 3% to 27% NR, underscoring its considerable research and economic significance. The myeloblastosis (MYB) transcription factor family, one of the largest in plants, plays pivotal roles in metabolic regulation, stress responses, and various growth and developmental processes. To identify key MYB transcription factors involved in hormone-induced rubber biosynthesis, we conducted homology-based and bioinformatic analyses to characterize 268 MYB family proteins in the TKS genome. Utilizing transcriptome data from jasmonic acid (JA) and ethylene (ET) treatments, we screened and shortlisted 10 candidate TkMYB transcription factors. Through tissue-specific expression profiling, TkMYB7 was selected as the primary candidate. We confirmed that promoter analysis combined with yeast one-hybrid assays confirmed that TkMYB7 directly binds to and regulates the expression of acetyl-CoA acetyltransferase (TkACAT5), a key enzyme in the mevalonate (MVA) pathway. Furthermore, heterologous overexpression of TkMYB7 in Arabidopsis thaliana significantly enhanced seed germination and root development. These findings identify TkMYB7 as a novel transcriptional regulator linking JA and ET signaling pathways to rubber biosynthesis in TKS, representing a promising target for the genetic improvement of rubber yield. Full article

Helper component-proteinase (HC-Pro), encoded by tobacco vein banding mosaic virus (TVBMV), can cause various viral symptoms and even abortion. HC-Pro counteracts host-mediated inhibition by interfering with the accumulation of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, it is unclear whether the abortion phenotype of transgenic plants expressing HC-Pro is related to the abnormal expression of TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING cell factors (TCPs), which are involved in regulating fertility. In this study, the molecular mechanisms through which HC-Pro causes various sterile phenotypes in plants were investigated. Reverse transcription–quantitative polymerase chain reaction (RT–qPCR) and Northern blotting revealed that in HC-Pro transgenic plants, the expression levels of TCP4 and TCP24 significantly increased. The increased expression of TCP4 further upregulated LIPOXYGENASE2 (LOX2), a gene encoding a key enzyme in the synthesis of jasmonic acid (JA) precursors. Further studies confirmed that the aberrant expression of TCP3, TCP4 and TCP24 blocks the elongation of petals and anthers and that the aberrant expression of TCP4 and TCP24 blocks the release of pollen. This study demonstrated that HC-Pro affects the expression levels of the miR319-targeted genes TCP2, TCP3, TCP4, TCP10 and TCP24, thereby affecting the normal development of floral organs and resulting in plant abortion. Both tobacco and Arabidopsis thaliana were used as model systems in this study on virus-mediated fertility, which provides important information for understanding how viral pathogenicity affects the regulation of fertility in crops. Full article

Cyanidioschyzon merolae, an extremophilic unicellular red alga thriving in acidic hot springs at temperatures of 40–56 °C and pH 0.5–4.0, faces extreme oxidative stress conditions. This study presents a comprehensive genomic analysis of the carotenoid and vitamin E biosynthetic pathways, which are essential for antioxidant defense in this organism. Through comparative genomics using Arabidopsis thaliana sequences as queries, we identified and characterized genes encoding key enzymes involved in their metabolism. Our analysis reveals that C. merolae exclusively utilizes the methylerythritol-4-phosphate (MEP) pathway for isoprenoid biosynthesis and lacks a complete mevalonate (MVA) pathway. We identified eleven genes involved in terpenoid metabolism and seven genes specifically for carotenoid biosynthesis. Pigment analysis confirmed a streamlined carotenoid profile consisting solely of β-carotene, β-cryptoxanthin, and zeaxanthin, lacking the entire β,ε-branch and part of the β,β-branch. The complete tocopherol biosynthetic pathway produces exclusively α-tocopherol. The absence of the β,ε-carotenoid branch and the exclusive production of α-tocopherol demonstrate metabolic streamlining while maintaining antioxidant efficacy. These findings provide molecular blueprints for biotechnological applications, enabling targeted strategies to enhance antioxidant production through pathway optimization and metabolic engineering, while offering insights into developing stress-tolerant organisms and enhancing nutritional content in crops. Full article

Heat stress exacerbated by global warming severely impairs the growth and tea quality of the tea plant (Camellia sinensis). Trehalose is pivotal for regulating plant growth and enhancing stress resistance. However, the molecular characteristics, expression patterns, and regulatory mechanisms of trehalose metabolism genes in tea plants under heat stress remain unclear. Therefore, this study conducted a comprehensive investigation of trehalose metabolism genes in the Tieguanyin tea plant genome. A total of 30 trehalose metabolism genes were identified, including 17 trehalose-6-phosphate synthase (CsTPS), 9 trehalose-6-phosphate phosphatase (CsTPP), and 4 trehalase (CsTRE) genes. These genes were characterized in terms of their chromosomal locations and gene structures; the encoded proteins were characterized in terms of their phylogenetic relationships, conserved motifs, functional domains, physicochemical properties, and subcellular distributions. The results showed that these genes exhibit family-specific structural and functional features, laying a foundation for further functional studies. Collinearity analysis identified 20 homologous gene pairs between tea plants and Arabidopsis thaliana, significantly more than the 3 pairs with Oryza sativa, suggesting a closer evolutionary relationship with A. thaliana. Additionally, five intraspecific duplicated gene pairs were identified, all with Ka/Ks values < 1, indicating they have undergone strong purifying selection during evolution, leading to functional stability. Cis-acting element analysis revealed abundant stress-responsive, light-responsive, and phytohormone-responsive elements in the promoter regions of these trehalose metabolism genes, indicating their potential involvement in tea plant stress resistance regulation. Differential expression analyses under heat stress with exogenous trehalose treatment (CK: control, T: water-sprayed heat stress, TT: 5.0 mM trehalose-sprayed heat stress) identified six differentially expressed genes (DEGs). We further analyzed the expression patterns of these DEGs. Specifically, CsTPS1, CsTPS5, and CsTPS12 were increasingly upregulated in CK, T, and TT, respectively, while CsTPP1 and CsTPP2 were upregulated in TT relative to T. Additionally, CsTRE1, CsTRE2, and CsTRE4 showed downregulation in TT compared to T, though they were not classified as DEGs. These findings indicate that exogenous trehalose application modulates trehalose metabolism by promoting CsTPS and CsTPP expression while inhibiting CsTRE expression, thereby increasing endogenous trehalose content in tea plants under heat stress. Yeast heat stress tolerance assays confirmed that CsTPS1, CsTPS5, CsTPS12, and CsTPP1 enhanced yeast survival at 38 °C, verifying their function in improving organismal heat stress tolerance. In conclusion, these results clarify the roles of trehalose metabolism genes in tea plants’ heat stress response, demonstrating that exogenous trehalose modulates their expression to increase endogenous trehalose levels. This study provides a theoretical foundation for exploring trehalose-mediated heat stress resistance mechanisms and improving tea plant stress tolerance via genetic engineering. Full article