Search Results (863)

Selective pressure targeting male functions plays a crucial role in the evolution of floral morphological traits. In some angiosperm groups, flowers contain two or more sets of stamens that vary in size, color, and morphology, a phenomenon known as heteranthery. This reflects an evolutionary adaptation of stamens. However, the developmental basis and molecular mechanisms remain poorly understood. This study integrates transcriptomic and developmental approaches to elucidate the molecular and morphological mechanisms underlying intra-floral stamen differentiation in Cassia fistula L., an economic leguminous tree exhibiting heteranthery with three distinct stamen types: long stamens (LS), short stamens (SS), and degenerated stamens (St). We documented asynchronous stamen primordia initiation and development trajectories across stamen types. Transcriptomic profiling and protein–protein interaction analysis identified differentially expressed genes (DEGs) between filaments of the three stamen sets, with significant enrichment in brassinosteroid (BR) related pathways. CYP90D1 (Cf_f49903) and CYP90C1 (Cf_f56973) emerged as candidate genes related to stamen length differentiation in C. fistula. This study not only helped elucidate the developmental and genetic framework of heteranthery in C. fistula but also provided new insights for exploring floral organ evolution in leguminous plants. Full article

Novel targeted therapies have transformed spinal muscular atrophy from a condition with a predictable, severe course into a more heterogeneous disorder with a range of new clinical phenotypes and outcomes. The emergence of new phenotypes in spinal muscular atrophy is a recent development in the field. The introduction of new etiopathogenic pharmacological treatments have significantly altered the natural history of the disease, leading to previously unseen clinical presentations and outcomes. Materials and Methods: We observed a cohort of 104 patients (children and adolescents), considering the number of SMN2 gene copies, the use of respiratory ventilation support devices and gastrointestinal support, and finally, their evolution on clinical-functional scales with physical therapy and rehabilitation interventions. With the increasing availability of effective therapies for spinal muscular atrophy, outcome measurement in clinical practice and research requires highly sensitive and reliable tools. In this study, motor function was systematically evaluated using two validated scales—the Children’s Hospital of Philadelphia Infant Test of Neuromuscular Disorders (CHOP INTEND) and the Hammersmith Functional Motor Scale Expanded (HFMSE)—which are specifically designed to capture incremental changes in motor skills across the spectrum of SMA severity and age groups. Results: The median scores on the validated tools steadily increased over the 24 months of follow-up. Starting from 29 at baseline, the scores rose to 36 at 6 months, then to 39 at 12 months, 43 at 18 months, and 44.5 at 24 months. The Friedman test showed that these changes were statistically significant (p < 0.01). Moreover, each follow-up score was significantly higher than both the baseline and the previous time point (all p < 0.01), showing continuous improvement over time. Conclusions: These findings reveal that the development of new SMA phenotypes is closely linked to the stage of disease at which treatment is initiated. Earlier intervention consistently enables patients to acquire previously unattainable motor skills. Consequently, enhancing diagnostic precision and expediting therapy initiation is crucial for maximizing clinical benefits and facilitating optimal functional outcomes. Full article

Gene duplication, a major source of new genes in evolution, often occurs via reverse transcription of mRNA, leading to the integration of a retrocopy into a new genomic locus. Here, we performed an in-depth analysis of the evolutionary history of the e(y)2 gene in Metazoa. The E(y)2 protein is a shared subunit of two highly conserved complexes involved in transcription regulation (the DUB module of the SAGA complex) and mRNA transport (TREX-2). In Deuterostomes, the e(y)2 gene has undergone multiple independent retropositions, often giving rise to functional retrogenes. In contrast, among Protostomes, duplications of e(y)2 were identified only in Drosophilinae and a member of the Lepidoptera family (Manduca sexta). In Drosophila, the retrocopy e(y)2 acquired an almost ubiquitous expression pattern and compensates for the function of the parental gene in all tissues except the testes. The parental gene, e(y)2b, evolved a testis-specific expression pattern, lost the ability to incorporate into the DUB module, but retained nuclear envelope localization and the capacity to assemble into the TREX-2 complex. Knockout of the D. melanogaster e(y)2b gene resulted in reduced male fertility. Overall, our study highlights distinct evolutionary trajectories of the e(y)2 gene in Deuterostomes and Protostomes. 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

Transposable elements (TEs) are major components of plant genomes and play crucial roles in adaptive genome evolution and stress tolerance. Under abiotic stress, activated TEs can generate abundant genetic variation and regulate the expression of stress-responsive genes. As a pioneer species in desert and saline–alkali environments, Tamarix chinensis L. has been little studied with respect to the abundance and evolutionary relationships of its LTR retrotransposons, particularly their activation patterns under salt and alkali stresses. This study aimed to investigate the characteristics of the reverse transcriptase (RT) domain of LTR retrotransposons in T. chinensis and to determine their patterns of activation in response to salt and alkali stresses. A total of 629 Ty1-copia and 607 Ty3-gypsy RT nucleotide sequences, which displayed high AT/GC ratios and evidence of stop codon insertions, were identified in T. chinensis by amplicon sequencing. Among these, 211 Ty1-copia and 117 Ty3-gypsy RT sequences with potential transpositional activity each contained distinct domains, suggesting a high degree of conservation. Phylogenetic analysis revealed that the RT sequences of T. chinensis are closely related to those of mangrove, wild potato, and Ipomoea, and may have undergone horizontal transfer. Expression analysis showed that 634 and 181 RT sequences were activated under salt and alkali stresses, respectively, with the majority belonging to salt-induced Ty1-copia families. Compared with the control group, under salt and alkali stresses, the cTy1-copia elements (Ty1-copia with amplificated from cDNA of T. chinensis, the same below) with dominant abundance were mainly concentrated in the Angela subfamily, while the cTy3-gypsy elements induced by alkali stress were primarily distributed in the Tekay and Reina subfamilies. Furthermore, four cTy1-copia and five cTy3-gypsy were identified as candidate key LTR retrotransposons responsive to salt and alkali stresses. Overall, this study provides new insights into the epigenetic mechanisms underlying the adaptation of T. chinensis to saline and alkali stresses and offers a theoretical basis for its potential applications in saline–alkali land reclamation. Full article

Gene regulatory networks (GRN) govern cellular identity and function through precise control of gene transcription. Single-cell technologies have provided powerful means to dissect regulatory mechanisms within specific cellular states. However, existing computational approaches for modeling single-cell RNA sequencing (scRNA-seq) data often infer local regulatory interactions independently, which limits their ability to resolve regulatory mechanisms from a global perspective. Here, we propose a deep learning framework (Planet) based on diffusion models for constructing cell-specific GRN, thereby providing a systems-level view of how protein regulators orchestrate transcriptional programs. Planet jointly optimizes local network structures in conjunction with gene expression profiles, thereby enhancing the structural consistency of the resulting networks at the global level. Specifically, Planet decomposes GRN generation into a series of Markovian evolution steps and introduces a Triple Hybrid-Attention Transformer to capture long-range regulatory dependencies across diffusion time-steps. Benchmarks on multiple scRNA-seq datasets demonstrate that Planet achieves competitive performance against state-of-the-art methods and yields only a slight improvement over DigNet under comparable conditions. Compared with conventional diffusion models that rely on fixed sampling schedules, Planet employs a fast-sampling strategy that accelerates inference with only minimal accuracy trade-off. When applied to mouse-lung Cd8⁺Gzmk⁺ T cells, Planet successfully reconstructs a cell-type-specific GRN, recovers both established and previously uncharacterized regulators, and delineates the dynamic immunoregulatory changes that accompany ageing. Overall, Planet provides a practical framework for constructing cell-specific GRNs with improved global consistency, offering a complementary perspective to existing methods and new insights into regulatory dynamics in health and disease. Full article

Background/Objectives: Plant mitogenomes display remarkable variation in size, structure, and gene content, yet their evolutionary causes remain unclear. Araceae, the most significant family within Alismatales, encompasses both aquatic and terrestrial lineages, providing an excellent system for studying how ecological shifts influence mitogenome evolution. Methods: We assembled and annotated four new mitogenomes using both short- and long-read sequencing, including three aquatic taxa (Pistia stratiotes L., Spirodela intermedia W. Koch, Wolffia australiana (Benth.) Hartog & Plas) and one terrestrial species (Amorphophallus konjac K. Koch). Along with five previously published mitogenomes, we performed comparative analyses across nine Araceae species. Results: These mitogenome sizes varied from ~178 kb to ~877 kb, consisting of one to 19 circular molecules, with aquatic species generally having smaller and simpler structures. Plastid-derived sequences (MTPTs) contributed 1.2–10.6% of genome content, peaking in Zantedeschia aethiopica (L.) Spreng. Despite significant structural heterogeneity, all species maintained core respiratory genes under strong purifying selection, while ribosomal protein-coding genes showed lineage-specific loss. RNA editing ranged from 363 to 772 sites per mitogenome, with the number of sites independent of mitogenome size. Conclusions: Overall, this study uncovers the dynamic evolutionary patterns of Araceae mitogenomes and offers a framework for understanding how habitat shifts between aquatic and terrestrial environments influence mitogenome diversity in plants. Full article

Cryptic species are morphologically indistinguishable but possess genetically distinct taxa. Alternative splicing (AS) regulates physiological processes, thereby facilitating ecological adaptation and evolution. To explore the sex-specific differences in transcriptional regulation among cryptic species, we profiled both AS and gene expression in two cryptic species of Wiebesia pumilae (WPDZ19 and WPHS), which differ in Wolbachia infection status. The results showed that 101 and 71 differentially alternatively spliced genes (DASs) were identified in female and male groups, respectively. Functional enrichment revealed that female DASs were significantly enriched in mitotic cell cycle process, cytoskeleton organization, cellular component organization, and DNA damage. On the other hand, male DASs were predominantly related to actin, cytoskeleton, and muscle development. Gene set enrichment analysis of DASs also revealed that the regulation of mitotic nuclear division and meiotic nuclear division were enriched in female and male groups, respectively. We identified 4509 DEGs in females and 3645 in males, with minimal overlap between DASs and DEGs. Moreover, RT-PCR has been used to validate the key genes. Our results revealed sexually divergent transcriptional regulation patterns between WPDZ19 and WPHS, suggesting a potential association with Wolbachia persistence. Our findings provide new insights into the study of adaptive evolution of cryptic species. Full article

Safflower (Carthamus tinctorius L.) is a multipurpose economic crop. Flavonoid glycosides are its key bioactive constituents, and several glycosyltransferases involved in their biosynthesis have been identified. The glycosyltransferase 84 subfamily represents a specialized branch with diverse functions, involved not only in catalyzing flavonoid glycosylation but also in the biosynthesis of auxins, tannins, and other compounds. However, this subfamily remains poorly characterized in safflower. In this study, two UGT84 subfamily genes, UGT84A28 and UGT84B3, were screened based on expression patterns and phylogenetic evolution analysis. Recombinant proteins were induced and purified using prokaryotic expression systems. Functional characterization was subsequently conducted through enzymatic assays in vitro and transient expression in tobacco leaves. Molecular docking was employed to investigate the binding modes of UGTs with UDP-glucose. The results indicated that both UGTs demonstrated glycosylation activity at the flavonoid 7-OH position. Notably, when luteolin was employed as the aglycone, both enzymes also exhibited 3′-O-glycosylation activity. Combined with amino acid sequence alignment, we propose that residues A351/T343 and G263/F254, which affect spatial conformation and hydrogen bonding ability, may be one of the reasons for the functional differences between these two enzymes. These findings provide new insights into the catalytic diversity of glycosyltransferases. Full article

Antibiotic resistance remains one of the most formidable challenges to modern medicine, threatening to outpace therapeutic innovation and undermine decades of clinical progress. While resistance was once viewed narrowly as a clinical phenomenon, it is now understood as the outcome of complex ecological and molecular interactions that span soil, water, agriculture, animals, and humans. Environmental reservoirs act as silent incubators of resistance genes, with horizontal gene transfer and stress-induced mutagenesis fueling their evolution and dissemination. At the molecular level, advances in genomics, structural biology, and systems microbiology have revealed intricate networks involving plasmid-mediated resistance, efflux pump regulation, integron dynamics, and CRISPR-Cas interactions, providing new insights into the adaptability of pathogens. Simultaneously, the environmental dimensions of resistance, from wastewater treatment plants and aquaculture to airborne dissemination, highlight the urgency of adopting a One Health framework. Yet, alongside this growing threat, novel therapeutic avenues are emerging. Innovative β-lactamase inhibitors, bacteriophage-based therapies, engineered lysins, antimicrobial peptides, and CRISPR-driven antimicrobials are redefining what constitutes an “antibiotic” in the twenty-first century. Furthermore, artificial intelligence and machine learning now accelerate drug discovery and resistance prediction, raising the possibility of precision-guided antimicrobial stewardship. This review synthesizes molecular insights, environmental drivers, and therapeutic innovations to present a comprehensive landscape of antibiotic resistance. By bridging ecological microbiology, molecular biology, and translational medicine, it outlines a roadmap for surveillance, prevention, and drug development while emphasizing the need for integrative policies to safeguard global health. Full article

The microhylid frog Microhyla fissipes is a protected terrestrial wildlife species in China, recognized for its ecological, economic, and scientific value. However, its mitochondrial genome remains poorly characterized. To address this gap, we sequenced and annotated the complete mitogenome of M. fissipes to elucidate its structural organization and phylogenetic placement within Microhylidae. The assembled mitogenome is 16,723 bp in length and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, and 22 tRNAs, along with one control region and the origin of heavy-strand replication. We also identified eight overlapping regions and eleven intergenic spacers. The overall base composition showed an A + T bias (59.91%) with negative AT-skew (−0.04) and GC-skew (−0.27). All tRNAs displayed typical cloverleaf secondary structures, except for trnS1, which lacked the D-arm. Phylogenetic reconstruction using both maximum likelihood and Bayesian inference strongly supported the monophyly of Microhylidae and revealed a sister-group relationship between Microhyla and Kaloula. Within Microhyla, M. fissipes was most closely related to M. heymonsi, with which it formed a well-supported clade that also included Microhyla okinavensis, Microhyla mixtura, and Microhyla beilunensis. Selection pressure analysis on protein-coding genes indicated widespread purifying selection (Ka/Ks < 1) across most genes, except for ATP8, COX2, and COX3, which may be under relaxed selective constraints. These findings offer valuable genomic resources for the conservation of M. fissipes and provide new insights into the phylogeny and evolution of microhylid frogs. Full article

Background: Pseudorabies virus (PRV), a critical porcine herpesvirus, induces severe diseases in both livestock and wildlife, imposing an incalculable burden and economic losses in livestock production. In this study, we investigated the evolutionary mechanisms and host adaptation strategies of the PRV gB gene through genomic alignment. The gB gene is highly conserved in PRV, and its encoded gB protein exhibits functional interchangeability across different herpesvirus species. Notably, the gB protein elicits the production of both complement-dependent and complement-independent neutralizing antibodies in animals, while also being closely associated with syncytium formation. Methods: Phylogenetic analysis and codon usage pattern analysis were performed in this study. A total of 110 gB gene sequences were analyzed, which were collected from [2011 to 2024] across the following regions: [Fujian, Shanxi, Guangxi, Guangdong, Chongqing, Henan, Shaanxi, Heilongjiang, Sichuan, Jiangsu, Jilin, Huzhou, Shandong, Hubei, Jiangxi, Beijing, Shanghai, Chengdu (China)], [Budapest, Szeged (Hungary)], [Tokyo (Japan)], [London (United Kingdom)], [Athens (Greece)], [Berlin (Germany)], and [New Jersey (United States)]. Results: The gB gene of PRV employs an evolutionary “selective optimization” strategy to maintain a dynamic balance between ensuring functional expression and evading host immune pressure, with this core trend strongly supported by its codon usage bias and mutation characteristics. First, the gene exhibits significant codon usage bias [Effective Number of Codons (ENC) = 27.94 ± 0.1528], driven primarily by natural selection rather than mere mutational pressure. Second, phylogenetic analysis shows that the second codon position of gB has the highest mutation rate (1.0586)—a feature closely linked to its antigenic variation and immune escape capabilities, further reflecting adaptive evolution against host immune pressure. Additionally, ENC-GC3 plot analysis reveals the complex regulatory mechanisms underlying codon bias formation, providing molecular evidence for the “selective optimization” strategy and clarifying PRV’s core evolutionary path to balance functional needs and immune pressure over time. Conclusions: Our study findings deepen our understanding of the evolutionary mechanisms of PRV and provide theoretical support for designing vaccines and assessing the risk of cross-species transmission. Full article

Objectives: The Taihe Black-Boned Silky Fowl (TBSF) is a unique indigenous chicken breed in China, characterized by widespread melanin deposition throughout its body. Fluoroquinolones (FQs) such as enrofloxacin can persist in TBSF for an extended period exceeding 100 days. The aim of this study was to examine the current status and development trends of FQ resistance within the TBSF breeding environment. Methods: Whole-genome sequencing was utilized to identify the molecular presence of quinolone resistance-determining region (QRDR) mutations and plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli isolates obtained from TBSF farms. Network inference based on strong Spearman correlations (ρ > 0.5) and statistically significant associations (p-value < 0.05) was applied to investigate the co-occurrence patterns among FQ residues, resistance phenotypes, and antibiotic resistance genes. Results: The results showed that FQ residues were identified as the primary contributor to FQ resistance in E. coli isolates. Mutations at QRDR sites were the predominant factor driving FQ resistance, rather than PMQR determinants. This study also reported the first identification of GyrA-S83Q mutation being associated with FQ resistance. Conclusions: It was concluded that E. coli strains in TBSF environments, where chickens have a long-term residual metabolic cycle of antimicrobials, may develop and evolve new mechanisms to adapt to this environment. Further research is warranted to investigate the evolution of FQ resistance in E. coli strains within TBSF environments. Full article

Soybean (Glycine max (L.) Merr.) flowering time and plant height are critical agronomic traits that significantly influence yield and environmental adaptability. To clarify the regulatory mechanisms of flowering-related genes and their associations with plant height, a genome-wide identification of such genes in soybean were performed. This analysis used Arabidopsis thaliana flowering genes as references, employing BLASTP searches and pathway classification. All of the identified flowering-related genes were classified into eight regulatory pathways, with the photoperiod pathway (Ph) being the most prominent. Evolutionary and expression analyses revealed that core regulators (e.g., GmFTs, GmSOC1s) are conserved across pathways and are preferentially expressed in shoot apical meristems (SAMs). Additionally, both flowering-related genes and key hormones (e.g., IAA, GA, ABA) exhibited rhythmic responses to light signals. CRISPR-Cas9-mediated validation confirmed that genes GmSAUR46b regulates both flowering time and plant height, as mutants of this gene showed early flowering and reduced height. Notably, a large proportion of previously mapped flowering genes overlapped with our identified ones, while some remained undetected, likely due to whole-genome duplication and adaptive evolution, which generate new regulatory networks. Most of the identified flowering-related genes, however, have not been mapped, which highlights substantial uncharacterized potential in soybean flowering and plant height regulation. This provides a valuable molecular framework to guide soybean molecular breeding for enhanced yield and environmental adaptability. Full article

The use of antibiotics is so widespread in animal husbandry, but negligent management and lack of policies often lead to the massive use of antibiotics on farms. In this study, we collected cases of epidemic calf diarrhea in northeastern China and isolated a new strain of multidrug-resistant Escherichia coli (MDR-E. coli). In order to explore the information of this pathogen in detail, we used whole-genome sequencing to determine the genome sequence, and explored in detail the resistance, pathogenicity, genetic evolution and other biological processes of the strain through bioinformatics analysis. The results showed that the E. coli isolated in this study was a new multidrug-resistant strain with a large number of drug resistance genes (77) and virulence genes (84), including a circular chromosome and five circular plasmids, which are basically impossible to treat by currently commonly used antibiotics. The findings of this study suggest that the prolonged misuse of antibiotics in agricultural settings may contribute to the development of antibiotic-resistant strains of E. coli. This, in turn, has the potential to trigger outbreaks of antibiotic-resistant bacterial diarrhea, leading to substantial economic losses and posing significant public health risks. These results underscore the necessity for the judicious use of antibiotics and will inform the development of pertinent policies and regulations. Full article