Search Results (3,592)

Background: Polyploidization drives the formation and evolution of angiosperms, profoundly reshaping genomic architecture and function. The 14-3-3 proteins (also known as G-box binding regulators, GRFs) are conserved signaling molecules involved in a range of physiological processes, including developmental signaling and stress responses. Elucidating the evolutionary trajectories of 14-3-3 genes in Brassica napus following allopolyploidization is critical for understanding polyploid crop evolution and developing molecular breeding strategies for improved stress resistance and yield. Results: In this study, forty-eight orthologous 14-3-3 genes were identified in the genome of B. napus, and twenty-two orthologous 14-3-3 genes were found in the genomes of both Brassica rapa and Brassica oleracea. Gene mapping analysis indicated that 14-3-3 genes were broadly distributed across all chromosomes; however, they exhibited significant heterogeneity. Phylogenetic tree construction revealed that 14-3-3 genes can be categorized into two groups: epsilon and non-epsilon genes. Gene structure analysis showed that most non-epsilon genes contain 3-4 exons, while most epsilon genes contain 5-7 exons. Collinearity analysis identified 36 orthologous gene pairs between the A (B. rapa) and C genomes (B. oleracea) but only 28 paralogous gene pairs within the A and C subgenomes of B. napus, indicating that some collinear 14-3-3 genes were lost during allopolyploidization. The Ka/Ks ratios (ratio of non-synonymous to synonymous substitution rate) of the 61 identified duplicated gene pairs were all less than 1, suggesting that these genes underwent purifying selection. Promoter analysis indicated that the average number of cis-acting elements in B. napus 14-3-3 genes was one more than in B. rapa and B. oleracea, implying that allopolyploidization increased the regulatory complexity of 14-3-3 genes. Tissue expression profiling demonstrated that the expression pattern of GRF2 homologs was altered after allopolyploidization. Conclusions: By systematically investigating the copy number, genomic distribution, structure, evolutionary relationships, and expression patterns of 14-3-3 genes in B. napus and its progenitors, this study enhances our understanding of how allopolyploidization promotes gene family evolution. Full article

The ongoing evolution of SARS-CoV-2 has given rise to variants with enhanced transmissibility and pathogenicity, many of which harbor mutations in the receptor-binding domain (RBD) of the viral spike protein. These mutations often confer increased viral fitness and immune evasion by modulating interactions with the human ACE2 receptor (hACE2) and escaping neutralizing antibodies. Accurate prediction of the functional consequences of such mutations—particularly their effects on receptor binding and antibody escape—is critical for assessing the public health threat posed by emerging variants. In this study, we apply a Mutation-dependent Biomacromolecular Quantitative Structure–Activity Relationship (MB-QSAR) framework to quantitatively model the biochemical phenotypes of RBD variants. Trained on comprehensive deep mutational scanning (DMS) datasets, our models exhibit strong predictive performance, achieving correlation coefficients (r²) exceeding 0.8 for hACE2 binding affinity and 0.7 for antibody neutralization escape. Importantly, the MB-QSAR approach generalizes well to multi-mutant variants and currently circulating lineages. Structural analysis based on model-derived interaction profiles offers mechanistic insights into key RBD–ACE2 and RBD–antibody interfaces, helping the rational design of broadly protective vaccines and therapeutics. This work establishes MB-QSAR as a rapid, accurate, and interpretable tool for the prediction of protein–protein interaction and forecasting viral adaptation, thereby facilitating early risk assessment of novel SARS-CoV-2 variants. Full article

After intensive artificial selection, the development of celestial eyes in goldfish involves the eyeballs protuberating and turning upwards. Thus, the celestial eye goldfish is an excellent model for both evolutionary and human ocular disease studies. Here, two mapping populations of goldfish with segregating eye phenotypes in the offspring were constructed. Through whole-genome sequencing and RNA-seq for eyeball samples, a premature stop codon in Exon 38 of the LRP2 gene was identified as the top candidate mutation for the celestial eye in goldfish. Fatty acid metabolism and epidermal cells, especially keratocyte-related functions, were inhibited in the eyeballs of celestial eye goldfish, while inflammatory reactions and extracellular matrix secretions were stimulated. These results suggest the dysfunction of the cornea in the celestial eye goldfish, and the same for the retina, which could be the results of the truncated LRP2 protein. In addition, the same gene, LRP2, is in charge of similar phenotypes (celestial eye and telescope eye) in goldfish, but these phenotypes have no shared mutations. In conclusion, the candidate mutation for the celestial eye in goldfish was identified by this study for the first time, and parallel evolutions of similar phenotypes at the molecular level under artificial selection were observed. These findings provide insights into the developmental and evolutionary processes of morphological changes in the eyes of goldfish. Full article

The TCP gene family plays essential roles in plant growth, development, and stress responses, yet their evolutionary dynamics and functional characteristics remain poorly understood in Juglandaceae species. Here, we aimed to systematically identify, classify, and characterize TCP genes across three nut-producing Juglandaceae species—Carya illinoinensis, Annamocarya sinensis, and Juglans regia—to elucidate their evolutionary relationships and potential functions in fruit development. We identified 44, 35, and 36 TCP genes in C. illinoinensis, A. sinensis, and J. regia, respectively, and classified them into three subfamilies (PCF, CIN, and CYC/TB1). Physicochemical property analysis revealed that most proteins were hydrophilic but relatively unstable. Conserved motif and gene structure analyses showed strong similarity among closely related members, while promoter regions were enriched with cis-acting elements associated with development, hormone signaling, and stress responses. Chromosomal mapping demonstrated an uneven distribution of TCP genes, with frequent clustering, and synteny analysis indicated strong conservation and gene duplication within and across species. Transcriptome profiling revealed that approximately half of the TCP genes were expressed in fruit tissues, with CIN subfamily members showing preferential expression. qRT-PCR validation further highlighted AsTCP23, CiTCP14, and JrTCP09 as highly expressed during fruit development, suggesting potential regulatory roles in fruit maturation. These findings provide new insights into the evolutionary patterns and functional divergence of TCP genes in Juglandaceae and establish a valuable foundation for future studies on fruit development and genetic improvement. Collectively, these findings advance our understanding of TCP gene evolution and provide potential molecular targets for improving fruit development and nut quality in Juglandaceae crops. Full article

The stingless bee Meliplebeia beccarii, endemic to Ethiopia, plays a crucial ecological and economic role through pollination and high-quality honey production. However, habitat degradation and anthropogenic pressures threaten its survival. In this study, we present the complete mitochondrial genome (mitogenome) of M. beccarii, revealing a compact structure of 15,458 bp with 13 protein-coding genes (PCGs), 19 tRNAs, and two rRNAs, characterized by an A + T bias (83.9%). Unique features include the absence of trnI, trnK, and trnA, translocation of trnQ and a novel inversion in the trnT-trnP combination. These findings highlight species-specific genomic adaptations. Phylogenetic analysis based on concatenated PCGs places M. beccarii within the Apidae lineage, contributing to a deeper understanding of stingless bee evolution. Our results underscore the utility of mitogenomic studies in biodiversity conservation and evolutionary biology, providing foundational insights for the management and preservation of M. beccarii. Full article

Rhododendron hainanense Merr. is a tropical flowering shrub valued for its strong orna-mental and medicinal properties; however, its horticultural application is limited by its susceptibility to waterlogging disasters. The AP2/ERF transcription factor family plays crucial roles in plant growth, development, and responses to biotic and abiotic stresses; however, its regulatory mechanism in response to waterlogging stress remains unclear. This study conducted a genome-wide analysis of the AP2/ERF transcription factor family in R. hainanense, identifying 142 RhAP2/ERFs genes distributed across 13 chromosomes and classified into five subfamilies. Conserved motif analysis confirmed the characteristic AP2 domain structure. Gene duplication events revealed 16 segmental duplication pairs, indicating a potential role in adaptive evolution. Cis-element and protein interaction analyses suggested involvement in abiotic stress responses. Transcriptome and qRT-PCR results under waterlogging stress showed significant up-regulation of RhERF9 and RhERF95, with RhERF9 expression increasing 130-fold after 3 days, implying a positive regulatory role for the RhERF9 protein in early waterlogging response. Tissue-specific expression highlighted RhERF9’s strong induction in roots, associated with aerenchyma formation and hypoxia adaptation. The identified candidate AP2/ERF genes in R. hainanense play important roles in abiotic stress resistance and lay a foundation for future applications in breeding and horticulture. 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

The growing interest in functional foods has driven research into protein hydrolysates produced by enzymatic hydrolysis, especially from agro-industrial by-products. These compounds stand out for their antioxidant, antihypertensive, and other bioactive properties, which are relevant to the food, pharmaceutical, and nutraceutical industries. In this context, a bibliometric analysis of 1498 articles indexed in the Web of Science (WoS) database (2015–2025, collected up to June) was conducted to map the evolution of knowledge, identify consolidated and emerging thematic lines, and recognize the most influential actors in the field. The methodology combined an advanced search strategy with Biblioshiny (RStudio) and VOSviewer to generate co-occurrence maps, collaboration networks, and citation analyses. The results show sustained growth since 2018, with a predominance of research on functional properties, bioactive peptides, and antioxidant activity, along with a growing interest in sustainability, process optimization, and in silico methodologies. Six thematic clusters were identified, encompassing process optimization, biofunctional validation, circular economy, and non-conventional protein sources. The study concludes that the field demonstrates significant thematic maturity, with opportunities for innovation, particularly in functional validation and the integrated use of by-products through sustainable enzymatic technologies. Full article

Caleosins (CLOs) or peroxygenases (PXGs), a class of structural proteins of lipid droplets (LDs), comprise a small family of multifunctional proteins widely involved in oil accumulation, organ development, and stress responses. Despite the proposal of two clades termed H and L in Arabidopsis thaliana, their evolution in the order Brassicales has not been well established. In this study, the first genome-wide analysis of the caleosin family was conducted in papaya (Carica papaya), a Caricaceae plant without any recent whole-genome duplication (WGD). A high number of five members representing both H and L clades were identified from the papaya genome. Further identification and comparison of 68 caleosin genes from 14 representative plant species revealed seven orthogroups, i.e., H1–4 and L1–3, where H1 and L1 have already appeared in the basal angiosperm Amborella trichopoda, supporting their early divergence before angiosperm radiation. Five CpCLO genes belong to H1 (1) and L1 (4), and extensive expansion of the L1 group was shown to be contributed to by species-specific tandem and transposed duplications, which may contribute to environmental adaptation. Orthologous and syntenic analyses uncovered that lineage-specific expansion of the caleosin family in Brassicales relative to A. trichopoda was largely contributed to by tandem duplication and recent WGDs, as well as the ancient γ whole-genome triplication (WGT) shared by all core eudicots. Independent gain or loss of certain introns and apparent expression divergence of caleosin genes were also observed. Tissue-specific expression analysis showed that CpCLO2 and −5 are constitutively expressed, whereas others appear to be tissue-specific, implying function divergence. Interestingly, the H-forms CpCLO1 and RcCLO1 were shown to exhibit similar expression profiles to most oleosin genes that are preferentially expressed oil-rich tissues such as seeds/endosperms, shoots, and calluses, implying their putative involvement in oil accumulation, as observed in Arabidopsis. The results obtained from this study provide a global view of CpCLO genes and insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in papaya and other non-model species. Full article

Phosphates are essential nutrients for living organisms, and they are involved in various biological processes, including lipid metabolism, energy synthesis, and signal regulation. Recent studies have elucidated the fundamental components and transport proteins of phosphate signaling pathways, thereby providing a more profound understanding of phosphate metabolism in fungi. In this review, we concentrate on synthesizing the recent findings concerning phosphate metabolism in fungi over the past five years. These findings include the role of phosphates in the global phosphorus cycle, their effect on fungal growth and development, the variations in PHO signaling pathways among different species, and their pivotal role in symbiosis with plants. A mounting body of research substantiates the notion that phosphates play a pivotal role in regulating fungal life activities through a multifaceted mechanism. This regulatory function encompasses the promotion of growth and development, adaptation to environmental variations among different fungal species, and the evolution of distinct regulatory factors and transport proteins. Consequently, this fosters fungal diversity. Full article

Background/Objectives: Proliferative verrucous leukoplakia (PVL) is an oral potentially malignant disorder characterized by a high risk for cancer development. Current evidence suggests that the evolution and malignant transformation of PVL is driven by a reciprocal crosstalk between the epithelial cells and the subepithelial immune microenvironment. The aim of the present study was to compare for the first time the immunohistochemical expression of the immune response-related proteins GATA-binding protein 3 (GATA3), c-KIT/cluster of differentiation (CD)117, CD56 and CD45 between PVL, PVL-associated oral squamous cell carcinoma (OSCC) and solitary (localized) oral leukoplakia (OL) cases. Methods: Thirty-six formalin-fixed and paraffin-embedded tissue specimens were used; sixteen from 8 patients with PVL, ten from 10 patients with PVL-OSCC and ten from 10 patients with OL. Immunohistochemistry was conducted using monoclonal primary antibodies against GATA3, c-KIT/CD117, CD56 and CD45. A semi-quantitative method was applied to score staining, and statistical analysis included Wilcoxon signed-rank test, Kruskal–Wallis test with Dunn’s post hoc test and Spearman’s correlation coefficient test. Results: A significantly decreased GATA3 expression was found in PVL-OSCC cases compared with PVL and OL cases. c-KIT/CD117 and CD56 proteins were consistently expressed in all study groups, while a significantly higher CD45 expression was noted in PVL than OL. No significant correlation between markers was found. Conclusions: These data collectively underscore an activated yet disturbed immune response that might be involved in the development and progression of malignancy in PVL that may also be considered as unique and interesting in vivo model of oral carcinogenesis. Full article

This study conducted a genome-wide identification and systematic evolutionary analysis of the banana WRKY gene family using bioinformatics, transcriptomics, and molecular biology approaches. A total of 153 WRKY genes were identified in the banana genome, with significant differences in the amino acid count, molecular weight, and other physicochemical properties of their encoded proteins. The subcellular localization of these proteins is primarily in the nucleus. These genes are unevenly distributed across 11 chromosomes, with the highest density on chromosome 7. WRKY gene family members exhibit diverse expression patterns during fruit development and ripening, and some can respond to multiple abiotic and biotic stresses. Systematic evolutionary analysis classified them into three major groups (I, II, and III), with Group II having the highest number of members, which are further divided into five subgroups. Conserved motif analysis revealed that Motif1, Motif2, and Motif4 are key structural elements in the family’s evolution, with some members having a WRKYGKK variant. The gene structure shows a wide range of exon numbers (1–22), and the promoter regions are rich in cis-elements related to light response, hormone signaling, and stress response, indicating their potential for integrating light signals, hormone networks, and multiple stress responses. Collinearity analysis identified 116 segmental duplication events, with Ka/Ks values all less than 1, indicating purifying selection. After ethylene treatment, 51 genes showed significant changes in expression, which can be categorized into four patterns: sustained upregulation, sustained downregulation, initial upregulation followed by downregulation, and delayed upregulation. Among these, MaWRKY10, MaWRKY88, and MaWRKY137 exhibited significant expression changes and may play key roles in fruit ripening. These findings significantly contribute to the theoretical framework regarding the evolution and function of the WRKY family in plants. Moreover, they offer valuable gene resources and regulatory strategies that enhance postharvest banana preservation and molecular breeding efforts. Full article

Background: Ethylene is one of the most important plant hormones. ACC oxidase (ACO) plays a vital role in ethylene synthesis and responses to biotic and abiotic stresses in plants. However, its function in Triticum urartu remains unclear. This study aims to systematically identify the members of the TuACO gene family to elucidate its response characteristics and functions under biotic and abiotic stresses. Methods: Through homologous alignment, phylogenetic evolution analysis, and investigations of gene structure and promoter cis-elements, a total of eight TuACO genes were identified in the T. urartu genome based on their homology to OsACO and AtACO protein sequences. Results: These genes were classified into five ACO subfamilies and distributed across chromosomes 1A, 4A, 5A, 6A, and 7A. TuACO gene families contained 0–3 introns and 1–4 exons. The protein sequence contains 10 different conservative motifs. QRT-PCR expression analysis revealed that the transcript levels of TuACO5a, TuACO5b, and TuACO3a were significantly upregulated at 6 and 24 h after infection with powdery mildew, a biotic stress. Under boron deficiency, an abiotic stress, the expression of TuACO6 and TuACO1b increased, whereas the expression of TuACO5b and TuACO3b was markedly induced under high-boron conditions. Conclusions: These results demonstrate that TuACO genes exhibit functional diversification in response to biotic and abiotic stresses, which lays the foundation for elucidating their gene functions. Full article

Moonlighting proteins—single polypeptides performing multiple, often unrelated functions—are increasingly recognized as key players in human disease and microbial pathogenesis, making their identification crucial for understanding disease mechanisms and developing targeted therapies. This study addresses the unresolved question of how such multifunctionality evolves, focusing on two potential structural mechanisms: Non-Orthologous Gene Displacement/Non-Homologous Isofunctional Enzymes (NOGD/NHIE), where evolutionarily unrelated proteins perform the same function, and Fold-Switching Proteins (FSP), which adopt alternative secondary structures to switch functions without sequence changes. We analyzed the overlap between known human moonlighting proteins (from MultitaskProtDB-II) and curated datasets of NOGD/NHIE (Non-Orthologous Gene Displacement/Non-Homologous Isofunctional Enzymes) and fold-switching proteins (FSPs), using Fisher’s exact test for statistical validation. Moonlighting proteins showed extraordinary enrichment for NOGD/NHIE (19.89% vs. 0.39% in non-moonlighting proteins; odds ratio = 63.1, p < 2.2 × 10⁻¹⁶) and strong enrichment for FSPs (6.99% vs. 0.26%; odds ratio = 28.7, p = 1.13 × 10⁻¹⁴), corresponding to ~51-fold and ~27-fold higher risks, respectively. These findings establish intrinsic structural plasticity—whether through evolutionary replacement (NOGD/NHIE) or conformational switching (FSP)—as a central mechanism enabling functional moonlighting in the human proteome. The results suggest that such plasticity facilitates functional innovation while preserving sequence integrity, and that both NOGD/NHIE and FSP features may serve as predictive signatures for identifying novel moonlighting proteins, particularly those with implications for disease mechanisms and therapeutic targeting. Full article

Background/Objectives: The butterfish Stromateus stellatus is undervalued and usually discarded as bycatch, leading to an inefficient and unsustainable use of marine biomass. Overall, although Stromateus is the type genus of the family Stromateidae, its species are less studied than more economically important fishes. Methods: In this study, we determined and analyzed the complete mitochondrial genome sequence of S. stellatus. Furthermore, we performed maximum likelihood and Bayesian inference analyses to infer the phylogenetic relationships among 21 species of the order Scombriformes. Results: Using next-generation sequencing (NGS) and de novo assembly, a circular mitochondrial genome of 16,509 bp was obtained, exhibiting the typical vertebrate mitochondrial structure comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Three intergenic regions were identified, including the control region and the origin of light-strand replication, along with several gene overlaps. The heavy strand nucleotide composition was determined to be 28.79% A, 27.84% C, 16.32% G, and 27.05% T, with a GC content of 44.16%. The three Peprilus and five Pampus species formed a clade together with S. stellatus, supported by high bootstrap and posterior probability values, confirming the monophyly of Stromateidae. Conclusions: The gene order and content are consistent with those reported for other Stromateidae species and correspond to the typical arrangement observed in most bony fishes. This mitochondrial genome represents the first one reported for the genus Stromateus, providing valuable insights into the genetic makeup of S. stellatus, contributing to a better understanding of marine biodiversity. Additionally, these data will support future research on pelagic fish evolution and assist in sustainable fisheries management. Full article