Search Results (1,296)

Background: Transcription factors (TFs) critically regulate gene expression, orchestrating plant growth, development, and stress responses. The conserved IDD (INDETERMINATE DOMAIN) TF family modulates key developmental processes, including root, stem, and seed morphogenesis. Dendrocalamus latiflorus Munro, an economically vital sympodial bamboo in southern China, suffers significant yield losses due to prevalent bamboo shoot abortion, impacting both edible shoot production and timber output. Despite the documented roles of IDD TFs in shoot apical meristem expression and lateral organ regulation, their genome-wide characterization in D. latiflorus remains unstudied. Methods: Using IDD members from Arabidopsis thaliana, Oryza sativa, and Phyllostachys edulis as references, we identified 45 DlIDD genes in D. latiflorus. Comprehensive bioinformatics analyses included gene characterization, protein physicochemical assessment, phylogenetic reconstruction, and examination of gene structures/conserved domains. Differential expression of DlIDD genes was profiled between dormant and sprouting bamboo shoots to infer putative functions. Results: The 45 DlIDD genes were phylogenetically classified into three subfamilies and unevenly distributed across 34 chromosomes. Whole-genome duplication (WGD) events drove the expansion of this gene family. Promoter analyses revealed enriched cis-regulatory elements associated with hormone response and developmental regulation. Functional analyses suggested potential roles for DlIDD genes in bamboo shoot development. Conclusions: This study provides a foundation for future research to elucidate the functions of IDD TFs and their regulatory mechanisms in bamboo shoot morphogenesis and lateral bud development within woody monocots. Full article

Shiga toxin-producing Escherichia coli (STEC) are genetically diverse foodborne pathogens of major global public health concerns. Serogroup-level identification is critical for effective surveillance and outbreak control; however, it is often challenged by STEC’s genome plasticity and frequent recombination. In this study, we employed a standardized pangenomic pipeline integrating Roary ILP Bacterial Core Annotation Pipeline (RIBAP) and Panaroo to analyze 160 complete, high-quality STEC genomes representing eight major serogroups at a 95% sequence identity threshold. Candidate serogroup-specific markers were identified using gene presence/absence profiles from RIBAP and Panaroo. Our analysis revealed several high-confidence markers, including metabolic genes (dgcE, fcl_2, dmsA, hisC) and surface polysaccharide-related genes (capD, rfbX, wzzB). Comparative pangenomic evaluation showed that RIBAP predicted a larger pangenome size than Panaroo. Additionally, some genomes from the O104:H1, O145:H28, and O45:H2 serotypes clustered outside their expected clades, indicating sporadic serotype misplacements in phylogenetic reconstructions. Functional annotation suggested that most candidate markers are involved in critical processes such as glucose metabolism, lipopolysaccharide biosynthesis, and cell surface assembly. Notably, approximately 22.9% of the identified proteins were annotated as hypothetical. Overall, this study highlights the utility of pangenomic analysis for potential identification of clinically relevant STEC serogroups markers and phylogenetic interpretation. We also note that pangenome analysis could guide the development of more accurate diagnostic and surveillance tools. Full article

A comprehensive analysis of the molecular epidemiology of SARS-CoV-2 in the Kandy District of Sri Lanka from November 2020 to March 2022 was conducted to address the limited genomic surveillance data available across the country. The study investigated the circulating SARS-CoV-2 lineages, their temporal dynamics, and the associated mutational profiles in the study area. A total of 280 SARS-CoV-2-positive samples were selected, and 252 complete genomes were successfully sequenced using Oxford Nanopore Technology. Lineage classification was performed using the EPI2ME tool, while phylogenetic relationships were inferred through maximum likelihood and time-scaled phylogenetic trees using IQ-TREE2 and BEAST, respectively. Amino acid substitutions were analyzed to understand lineage-specific mutation patterns. Fifteen SARS-CoV-2 lineages were identified, and of those B.1.411 (36%) was the most prevalent, followed by Q.8 (21%), AY.28 (9.5%), and the Delta and Omicron variants. The lineage distribution showed a temporal shift from B.1.411 to Alpha, Delta, and finally the Omicron, mirroring the global trends. Time to the most recent common ancestor analyses provided estimates for the introduction of major variants, while mutation analysis revealed the widespread occurrence of D614G in the spike protein and lineage-specific mutations across structural, non-structural, and accessory proteins.Detection of the Epsilon variant (absent in other national-level studies) in November 2020, highlighted the regional heterogeneity viral spread. This study emphasizes the importance of localized genomic surveillance to capture the true diversity and evolution of SARS-CoV-2, to facilitate containment strategies in resource-limited settings. Full article

NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in the nitrate signaling response, plant growth and development, and abiotic stress responses. However, their functions have not been explored in sweet potato. In this study, we identified 7 NLPs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), 9 NLPs in the diploid relative Ipomoea trifida (2n = 2x = 30), and 12 NLPs in Ipomoea triloba (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological properties, chromosome localization, phylogenetic relationships, syntenic analysis maps, gene structure, promoter cis-acting regulatory elements, and protein interaction networks were systematically investigated to explore the possible roles of homologous NLPs in the nitrate signaling response, growth and development, and abiotic stress responses in sweet potato. The expression profiles of the identified NLPs in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting differences in the evolutionary trajectories of the hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato NLPs and offer more candidate genes for improving nitrogen use efficiency and increasing yield in cultivated sweet potato. Full article

Background: Raffinose synthase (RFS) plays a crucial role in plant growth and development, as well as in responses to biotic and abiotic stresses. However, its functions in Brassica napus remain poorly understood. Methods: To investigate the characteristics of the RFS gene family in B. napus (rapeseed), five Arabidopsis thaliana RFS gene sequences were used as references to identify thirteen RFS genes in B. napus, four in Brassica rapa, and six in Brassica oleracea. A comprehensive analysis was conducted, including molecular characteristics, phylogenetic relationships, conserved protein motifs, gene structures, and chromosomal localization. Results: BnaC02G0100500ZS was selected as a candidate gene due to its unique expression profile. Sequence alignment identified it as BnaRFS6, and subcellular localization revealed that its encoded protein is localized in the mitochondria. Overexpression of BnaRFS6 in rapeseed significantly affected the soluble sugar and starch content in the stalks, resulting in increased levels of fructose, glucose, and raffinose, and a decreased starch content. Conclusions: These findings highlight the role of BnaRFS6 in enhancing sugar metabolism in B. napus, particularly in relation to fructose, glucose, and raffinose accumulation. Understanding its potential function provides a foundation for improving the sugar content and taste of rapeseed stalks through genetic engineering in the future. Full article

B-box (BBX) transcription factors, which are specific to the plant kingdom, play a crucial role in regulating light-dependent growth, development, secondary metabolite biosynthesis, and the response to biotic and abiotic stresses. Despite their significance, there has been a lack of systematic investigation into the BBX gene family in Ginkgo biloba. In the present study, we identified nine BBX genes within the G. biloba reference genome, distributed across seven chromosomes, and classified them into four groups based on their phylogenetic relationships with the BBX gene families of Arabidopsis thaliana. Our analysis of gene structure, conserved domains, and motifs suggests that GbBBXs exhibit a high degree of conservation throughout evolutionary history. Additionally, synteny analysis revealed that dispersed duplication events have contributed to the expansion of the BBX gene family in G. biloba. An examination of cis-regulatory elements indicated that numerous GbBBX genes contain motifs associated with light, hormones, and stress, suggesting their potential roles in responding to these signals and environmental adaptation. Expression profiles obtained from RNA-Seq data and quantitative Real-Time PCR (qRT-PCR) analyses of GbBBX genes across various organs, hormone treatments, and leaves with differing flavonoid content, as well as during both short-term and long-term water stress, demonstrated their potential roles in flavonoid regulation and responses to hormones and water stress. Subcellular localization studies indicated that the proteins GbBBX5, GbBBX7, GbBBX8, and GbBBX9 are localized within the nucleus. This study is the first thorough analysis of the BBX gene family in G. biloba, providing a valuable foundation for further understanding their evolutionary context and functional roles in flavonoid regulation and responses to water stress. Full article

Background/Objectives: High-risk human papillomavirus (HPV) is the principal etiological agent of cervical cancer, with distinct genotype-specific oncogenic potential. While HPV type 16 is most frequently implicated in carcinogenesis, the role of other genotypes and their interaction with sexually transmitted infections and cervico-vaginal dysbiosis is gaining recognition. This study aimed to assess the genotype-specific distribution of high-risk HPV among HPV-positive women from Southern Croatia and examine associations with age and co-infections with selected microbial pathogens. Methods: We conducted a retrospective cross-sectional study on 1211 HPV-positive women (out of 3098 tested) from Split and Dalmatia County between 2023 and 2024. Cervico-vaginal swabs were tested using molecular and culture-based methods for 14 high-risk HPV genotypes and several pathogens, including Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, Gardnerella vaginalis, and other microorganisms. In the analysis, each detected HPV genotype was also treated as a distinct line-level observation. Genotypes were grouped by phylogenetic and carcinogenic profiles, and statistical analyses—including chi-square tests and multinomial logistic regression—were performed to evaluate associations with age and co-infections. Results: Among high-risk HPV-positive women, the most frequently detected high-risk HPV genotypes were HPV 16 (23.3%), HPV 31 (22.4%), and HPV 51 (13.5%). Notably, HPV 18 was less prevalent (8.1%) and occurred at a similar frequency to HPV 58 and 68. Although younger age was significantly associated with high-risk HPV positivity (p < 0.001), no significant differences in HPV genotype group distribution were observed between age groups; however, C. trachomatis and Streptococcus agalactiae were significantly more prevalent in women aged ≤29 years (p < 0.001 and p = 0.029, respectively). Multinomial regression revealed that C. trachomatis was negatively associated with 16-related and lower-risk genotypes, while G. vaginalis showed a positive association with 16-related types. Conclusions: There is a complex interplay between high-risk HPV genotypes and microbial co-infections, which means the broader cervico-vaginal microbiome has to be considered in HPV risk assessment. The findings highlight the need for extended genotyping and microbial screening to inform regional prevention strategies. Full article

Background: Vancomycin-resistant Enterococcus faecium (VREfm), particularly vanA-positive strains, represents a growing threat in hospital settings worldwide. These bacteria are able to survive under severe environmental conditions, including high temperatures and saline concentrations. High genome plasticity and advanced ability of inheriting antimicrobial resistance determinants defined the success of E. faecium as a hospital pathogen. Methods: This study presents the whole genomic characterization of vanA-positive VREfm isolates, analyzing 10 clinical isolates collected from three tertiary care hospitals in Moscow, Russia. Several typing approaches, including two MLST schemes and cgMLST profiles, were used to elucidate the relationship between the isolates. Phylogenetic analysis placed the isolates in context with global VREfm populations, demonstrating both local clonal expansion and possible international connections. Phenotypic and genomic antimicrobial resistance profiles were obtained, as well as data regarding the repertoire of virulence factors and plasmid content. Results: Whole genome sequencing revealed that all isolates belonged to the clinically significant CC17 lineage, specifically sequence types ST80 and ST552. Notably, two isolates possessed truncated Tn1546-type transposons lacking vanY and vanZ genes, representing a potentially emerging variant of the vanA operon in Russian clinical settings. A plasmid carrying a truncated vanA operon was reconstructed using long-read sequencing. Conclusions: The study highlights the utility of genomic investigation for tracking resistance mechanisms and strain dissemination, providing crucial baseline data for epidemiological surveillance of infections caused by VREfm in Russia. These findings emphasize the need for continued genomic monitoring to understand the evolution and spread of antimicrobial resistance in clinically important enterococcal lineages. Full article

Edwardsiella tarda is a zoonotic facultative intracellular bacterium whose impact on farm-raised amphibians is still poorly defined. We recovered seven strains from American bullfrogs (Aquarana catesbeiana) on four farms in Guangdong, China, and combined field surveillance with molecular and pathological investigations. Phylogenetic analysis of 16S rRNA and rpoB sequences confirmed species identity. Quantitative PCR of 192 apparently healthy frogs revealed intestinal carriage at every farm, with prevalence ranging from 39 to 77 percent and bacterial loads of 10⁵–10⁶ CFU/mL, indicating widespread subclinical colonisation. Virulence profiling demonstrated a conserved core gene set (gadB, mukF, citC, fimA, ompA) and accessory variation confined to the flagellar gene fliC. The strains resisted trimethoprim, ampicillin, and tetracyclines, yet remained susceptible to third generation cephalosporins, carbapenems, and most aminoglycosides. Infection trials showed that although very high inocula caused acute fatalities, an inoculum of 10⁸ CFU/mL was sufficient to induce persistent enteritis characterised by suppressed tight junction proteins, elevated cytokine expression, and marked intestinal damage. These findings demonstrate that E. tarda circulates silently in bullfrog culture, carries an amphibian adapted virulence profile and still responds to key antimicrobials, providing a baseline for risk assessment, surveillance, and targeted control in amphibian aquaculture. Full article

The miR156 family, crucial for phase transition and stress responses in plants, remains functionally uncharacterized in the ecologically and commercially important gymnosperm Larix kaempferi. This study systematically investigated L. kaempferi miR156 through phylogenetic analysis, structural prediction, expression profiling during somatic embryogenesis, and heterologous functional validation in Arabidopsis. Four MIR156 family members (LkMIR156s) were identified in Larix kaempferi, each with a characteristic stem-loop structure and highly conserved mature sequences. Computational predictions indicated that these LkMIR156s target four LkSPL family genes (LkSPL1, LkSPL2, LkSPL3, and LkSPL9). qRT-PCR analysis showed that mature LkmiR156s expression remained relatively low during early embryonic development but was significantly upregulated at the cotyledonary stage (21–42 days). Precursor transcript levels peaked earlier (around 28 days) than those of the mature LkmiR156, which remained highly expressed throughout cotyledonary embryo development. This sustained high expression coincided with cotyledon morphogenesis and embryonic dormancy. Functional validation via heterologous overexpression of LkMIR156b1 in Arabidopsis resulted in increased rosette leaf numbers (42.86% ± 6.19%) and individual leaf area (54.90% ± 6.86%), phenotypically consistent with the established role of miR156 in growth regulation. This study reveals the temporal expression dynamics of LkmiR156s during L. kaempferi somatic embryogenesis and its coordinated expression patterns with cotyledon development and embryonic dormancy. The functional conservation of the miR156-SPL module was confirmed in a model plant, providing key molecular insights into the developmental regulatory network of conifers. These findings offer potential strategies for optimizing somatic embryogenesis techniques in conifer species. Full article

The WUSCHEL-related homeobox (WOX) gene family is integral to plant growth and development. Here, we identified 14 CcWOX genes from the Cinnamomum camphora genome and analyzed their phylogeny, conserved features, and expression patterns. Phylogenetic inference grouped CcWOX into the Ancient, Intermediate, and WUS clades, consistent with other plant lineages. Expression profiling across seven tissues/organs, together with qRT-PCR validation, revealed tissue-biased expression for several members (e.g., floral or root enrichment), suggesting gene-specific roles during development. Using AlphaFold3, we predicted monomeric structures for CcWOX proteins and an interface model compatible with an interaction between CcWOX3 and CcLBD33. Consistently, bimolecular fluorescence complementation (BiFC) in Nicotiana benthamiana detected nuclear YFP signals for cEYFP-CcWOX3 + nEYFP-CcLBD33 relative to appropriate negative controls, confirming a physical interaction in plant cells. While these findings support a putative WOX–LBD interaction module in C. camphora, the regulatory functions remain to be established. Overall, this work provides a framework for dissecting the CcWOX family in C. camphora and illustrates how AI-assisted structure prediction can be integrated with cell-based assays to accelerate hypothesis generation in plant developmental biology. Full article

The genus Sargassum is taxonomically complex and poorly studied in the Eastern Tropical Pacific. We analyzed specimens collected along the Pacific coast of Central America and compared them with historical records and herbarium material to clarify species identities. Using detailed morphological analyses with molecular phylogenetic reconstruction based on concatenated ITS2 (Internal Transcribed Spacer 2) and COX3 (Cytochrome Oxidase Subunit 3) sequences, we identify two distinct morphotypes corresponding to two well-supported clades. One clade matches the morphology and molecular profile of Sargassum liebmannii. We provide the most comprehensive description of this species to date, including the first published ITS2 and COX3 sequences. Since Taylor’s 1945 work on the tropical Pacific of the Americas, S. liebmannii has been widely reported and considered the predominant species. It forms a genetic clade with other species from the Gulf of California; therefore, we propose a new section, Herporhizum/Sinicola. The second clade represents a previously unrecognized taxon from Central America, which we describe as a new species: Sargassum lacrucense, within the subgenus Sargassum, section Sargassum. Contrary to previous reports, Sargassum brandegeei—now recognized as Sargassum herporhizum—was not found in the region. This study underscores the importance of integrating morphological and molecular data to resolve Sargassum taxonomy in Central America. Full article

Somatic embryogenesis (SE) is a key plant regeneration technique involving the reprogramming of somatic cells into embryogenic structures. This developmental transition is regulated by complex genetic and epigenetic mechanisms, including post-translational modifications such as SUMOylation—the covalent attachment of small ubiquitin-like modifier (SUMO) proteins to target proteins, influencing their function, stability, and interactions. While SUMOylation is known to regulate plant development and stress responses, its role in SE has remained unknown. In this study, we investigated the involvement of the SUMOylation pathway in SE induction in Medicago truncatula. Using BLASTp analysis with known SUMO pathway proteins from Arabidopsis thaliana and Glycine max, we identified 10 homologous genes in M. truncatula. Phylogenetic relationships, gene structure, and conserved motif analyses confirmed their evolutionary conservation and characteristic domains. Expression profiling revealed significant upregulation of SUMO pathway genes—including Mt SUMO2, Mt SAE1-2, Mt SCE1a-b, Mt MMS21, and Mt PIAL2—in embryogenic cell lines during early SE induction. Additionally, in silico prediction of SUMOylation sites and SUMO-interacting motifs (SIMs) in 12 key SE regulatory proteins indicated a broad potential for SUMO-mediated regulation. These findings suggest that SUMOylation may contribute to the acquisition of embryogenic competence during somatic cell reprogramming in plants. Full article

Glutaredoxins (GRXs) are important proteins in plant development and environmental adaptation. Despite extensive characterization of GRX gene family members in various plant species, limited research has been conducted on the identification and functional analysis of GRXs in the economically important Solanaceae family pepper (Capsicum annuum). This study identified 35 typical GRX genes in pepper and categorized them into three distinct groups: CC-, CGFS-, and CPYC-type, based on the phylogenetic topology, which was consistent with motif or domain arrangement, and gene structures. Furthermore, the determination of ω values indicated that purifying selection was a significant factor in the evolutionary diversification of GRX genes in the eudicot family. Intra-genome investigations demonstrated that both segmental and tandem duplications were involved in the expansion of CaGRX genes. Moreover, examination of collinearity within the Solanaceae family revealed 53 orthologous pairs of GRX genes. Additionally, prediction of cis-regulatory elements and analysis of expression profiles revealed the significant involvement of GRX genes in plant stress response, specifically in relation to hypoxia and submergence. Subsequent subcellular localization examination suggested CaGRX may be involved in the endomembrane system and regulation of oxidative balance in plants. Collectively, these findings enhance our comprehension of the structural and functional properties of GRX in pepper, and establish a groundwork for subsequent functional characterization of the CaGRX genes. Full article

Background: Corynebacterium ulcerans is an emerging zoonotic pathogen capable of cau-sing diphtheria-like infections in humans. Objectives: we report, for the first time in Brazil, the detection and phenotypic/genomic characterization of three atoxigenic ST-339 strains isolated from domestic animals, including one with a ciprofloxacin resistance profile linked to double GyrA mutations (S89L, D93G). Methods: species identification was performed by MALDI-TOF MS, followed by in vitro antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses to predict virulence determinants, antimicrobial resistance genes, CRISPR–Cas systems, mobile genetic elements, and in silico structural analysis as well as phylogenetic reconstruction. Results: whole-genome sequencing confirmed species identity, revealed high genetic similarity, and identified distinct phylogenetic subclades, suggesting potential international dissemination. Genomic analyses showed conserved virulence determinants, such as incomplete pilus clusters, iron acquisition systems, and the pld gene, with the absence of the tox gene. Molecular modeling and dynamics simulations indicated that GyrA mutations disrupt critical ciprofloxacin–magnesium–water interactions, reducing binding stability. Mobile genetic elements, prophages, and CRISPR–Cas systems underscored the genomic plasticity of these isolates. Conclusions: these findings document a little-studied antimicrobial resistance mechanism in zoonotic C. ulcerans, highlighting the need for strengthened surveillance and further research on virulence and resistance, even in ato-xigenic strains. Full article