Search Results (405)

Background: Salmonella is a bacterium that causes foodborne infections. This study characterized two strains isolated from cheese and beef in Brazil using whole-genome sequencing (WGS). Objectives: We evaluated their antimicrobial resistance profiles, virulence factors, plasmid content, serotypes and phylogenetic relationships. Methods: DNA was extracted and sequenced on the NovaSeq 6000 platform; the pangenome was assembled using the Roary tool; and the phylogenetic tree was constructed via IQ-TREE. Results and Discussion: For contextualization and comparison, 3493 Salmonella genomes of Brazilian origin from NCBI were analyzed. In our isolates, both strains carried the aac(6′)-Iaa_1 gene, while only Schwarzengrund harbored the qnrB19_1 gene and the Col440I_1 plasmid. Cerro presented the islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5 and SPI-9, while Schwarzengrund also possessed SPI-13 and SPI-14. Upon comparison with other Brazilian genomes, we observed that Cerro and Schwarzengrund represented only 0.40% and 2.03% of the national database, respectively. Furthermore, they revealed that Schwarzengrund presented higher levels of antimicrobial resistance, a finding supported by the higher frequency of plasmids in this serovar. Furthermore, national data corroborated our findings that SPI-13 and SPI-14 were absent in Cerro. A virulence analysis revealed distinct profiles: the cdtB and pltABC genes were present in the Schwarzengrund isolates, while the sseK and tldE1 family genes were exclusive to Cerro. The results indicated that the sequenced strains have pathogenic potential but exhibit low levels of antimicrobial resistance compared to national data. The greater diversity of SPIs in Schwarzengrund explains their prevalence and higher virulence potential. Conclusions: Finally, the serovars exhibit distinct virulence profiles, which results in different clinical outcomes. Full article

White-Nose Syndrome (WNS) has devastated insectivorous bat populations, particularly in North America, leading to severe ecological and economic consequences. Despite extensive research, many aspects of the evolutionary history, mitochondrial genome organization, and metabolic adaptations of its etiological agent, Pseudogymnoascus destructans, remain unexplored. Here, we present a multi-scale genomic analysis integrating pangenome reconstruction, phylogenetic inference, Bayesian divergence dating, comparative mitochondrial genomics, and refined functional annotation. We show that P. destructans exhibits extensive mitochondrial genome rearrangements absent in its nonpathogenic relatives from the Leotiomycetes class, suggesting a potential link between mitochondrial evolution and pathogenic adaptation. Our divergence dating analysis reveals that P. destructans separated from its Antarctic relatives approximately 141 million years ago, before adapting to bat hibernacula in the Northern Hemisphere. Additionally, our refined functional annotation significantly expands the known functional landscape of P. destructans, revealing an extensive repertoire of previously uncharacterized proteins involved in carbohydrate metabolism and secondary metabolite biosynthesis—key processes that likely contribute to its pathogenic success. By providing new insights into the genomic basis of P. destructans adaptation and pathogenicity, our study refines the evolutionary framework of this fungal pathogen and creates the foundation for future research on WNS mitigation strategies. Full article

Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to understand their mechanisms of multidrug resistance, virulence factors, and mobile genetic elements (MGEs). Methods: Twelve C. indologenes isolates were identified, and their antibiotic susceptibility profiles were determined. Whole genome sequencing (WGS) was performed using a hybrid approach combining Illumina short-reads and Oxford Nanopore long-reads to generate complete bacterial genomes. The hybrid assembled genomes were subsequently analyzed to detect antimicrobial resistance (AMR) genes, virulence factors, and MGEs. Results: C. indologenes isolates were primarily recovered from urine samples of hospitalized elderly male patients with underlying conditions. These isolates generally exhibited extensive drug resistance, which was subsequently explored and correlated with genomic determinants. With one exception, CMCI13 showed a lower resistance profile (Multidrug resistance, MDR). Genomic analysis revealed isolates with genome sizes of 4.83–5.00 Mb and GC content of 37.15–37.35%. Genomic characterization identified conserved resistance genes (bla_IND-2, bla_CIA-4, adeF, vanT, and qacG) and various virulence factors. Phylogenetic and pangenome analysis showed 11 isolates clustering closely with Chinese strain 3125, while one isolate (CMCI13) formed a distinct branch. Importantly, each isolate, except CMCI13, harbored a large genomic island (approximately 94–100 kb) carrying significant resistance genes (bla_OXA-347, tetX, aadS, and ermF). The absence of this genomic island in CMCI13 correlated with its less resistant phenotype. No plasmids, integrons, or CRISPR-Cas systems were detected in any isolate. Conclusions: This study highlights the alarming emergence of multidrug-resistant C. indologenes in a hospital setting in Thailand. The genomic insights into specific resistance mechanisms, virulence factors, and potential horizontal gene transfer (HGT) events, particularly the association of a large genomic island with the XDR phenotype, underscore the critical need for continuous genomic surveillance to monitor transmission patterns and develop effective treatment strategies for this emerging pathogen. Full article

Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption. Full article

Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin. Methods: Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modelling, and pangenome analysis were performed to characterize resistance mechanisms. Results: A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent carbapenemase gene among the resistant isolates was bla_NDM, which was also present in a subset of susceptible strains. The resistant isolates exhibited a significantly higher burden of non-synonymous mutations in their siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modelling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in the resistant isolates, particularly in high-risk clones such as ST395 and ST512. Genes associated with toxin–antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group. Conclusions: Cefiderocol resistance in CPE appears to be multifactorial. NDM-type metallo-β-lactamases and missense mutations in siderophore uptake systems—especially in those encoded by fec, fhu, and cir operons—play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insights into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies. Full article

The Fabaceae family, the third-largest among flowering plants, is nutritionally vital, providing rich sources of protein, dietary fiber, vitamins, and minerals. Leguminous plants, such as soybeans, peas, and chickpeas, typically contain two to three times more protein than cereals like wheat and rice, with low fat content (primarily unsaturated fats) and no cholesterol, making them essential for cardiovascular health and blood sugar management. Since the release of the soybean genome in 2010, genomic research in Fabaceae has advanced dramatically. High-quality reference genomes have been assembled for key species, including soybeans (Glycine max), common beans (Phaseolus vulgaris), chickpeas (Cicer arietinum), and model legumes like Medicago truncatula and Lotus japonicus, leveraging long-read sequencing, single-cell technologies, and improved assembly algorithms. These advancements have enabled telomere-to-telomere (T2T) assemblies, pan-genome constructions, and the identification of structural variants (SVs) and presence/absence variations (PAVs), enriching our understanding of genetic diversity and domestication history. Functional genomic tools, such as CRISPR-Cas9 gene editing, mutagenesis, and high-throughput omics (transcriptomics, metabolomics), have elucidated regulatory networks controlling critical traits like photoperiod sensitivity (e.g., E1 and Tof16 genes in soybeans), seed development (GmSWEET39 for oil/protein transport), nitrogen fixation efficiency, and stress resilience (e.g., Rpp3 for rust resistance). Genome-wide association studies (GWAS) and comparative genomics have further linked genetic variants to agronomic traits, such as pod size in peanuts (PSW1) and flowering time in common beans (COL2). This review synthesizes recent breakthroughs in legume genomics, highlighting the integration of multi-omic approaches to accelerate gene cloning and functional confirmation of the genes cloned. Full article

Successfully breeding high-yield, lodging-resistant hybrid rice varieties is critical for ensuring food security. Two-line hybrid rice system plays an essential role in rice breeding, and 1892S, an important two-line sterile line, has contributed significantly to the development of over 100 hybrid rice varieties with superior agronomic traits, including lodging resistance. Despite its importance, a comprehensive understanding of the genomic basis underlying these traits in 1892S has been lacking due to the limitations of short-read sequencing technologies. To address this gap, we utilized advanced telomere-to-telomere (T2T) genome assembly techniques to generate a high-quality, gap-free genome of 1892S—the final genome comprises 12 complete chromosomes with 40,560 protein-coding genes. Comparative genomic analysis identified multiple known lodging resistance genes, including SD1, Sdt97, SBI, OsFBA2, APO1, and OsTB1, with unique allelic variations that may enhance resistance. The pan-genome analysis identified 2347 strain-specific genes in 1892S, further supporting its unique genetic advantages. This study represents the complete T2T genome assembly of a two-line sterile line and provides novel insights into the genetic foundation of lodging resistance in hybrid rice. This study highlights the genetic potential of 1892S in hybrid rice breeding and provides a model for the genomic analysis of other two-line sterile lines, offering valuable insights for improving in hybrid rice, including traits lodging resistance, yield stability, and adaptability, which are crucial for global food security. Full article

Background: The genus Enterococcus includes a diverse group of bacteria that are commonly found in the gastrointestinal tracts of humans and animals, as well as in various environmental habitats. Methods: In this study, Enterococcus lactis RB10, isolated from goat feces, was subjected to comprehensive genomic and functional analysis to assess its safety and potential as a probiotic strain. Results: The genome of E. lactis RB10, with a size of 2,713,772 bp and a GC content of 38.3%, was assembled using Oxford Nanopore Technologies (ONT). Genome annotation revealed 3375 coding sequences (CDSs) and highlighted key metabolic pathways involved in carbohydrate, protein, and amino acid metabolism. The strain was susceptible to important antibiotics, including ampicillin, chloramphenicol, tetracycline, and vancomycin, but exhibited resistance to aminoglycosides, a common trait in Enterococcus species with non-hemolytic activity. Genomic analysis further identified two intrinsic antimicrobial resistance genes (ARGs). The strain also demonstrated antimicrobial activity against Bacillus cereus DMST 11098 and Salmonella Typhi DMST 22842, indicating pathogen-specific effects. Key genes for adhesion, biofilm formation, and stress tolerance were also identified, suggesting that RB10 could potentially colonize the gut and compete with pathogens. Moreover, the presence of bacteriocin and secondary metabolite biosynthetic gene clusters suggests its potential for further evaluation as a biocontrol agent and gut health promoter. Conclusions: However, it is important to note that E. lactis RB10 was isolated from goat feces, a source that may harbor both commensal and opportunistic bacteria, and therefore additional safety assessments are necessary. While further validation is needed, E. lactis RB10 exhibits promising probiotic properties with low pathogenic risk, supporting its potential use in food and health applications. Full article

The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them—from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness. Full article

Chitin deacetylase (CDA) plays a pivotal role in converting chitin to chitosan, yet industrial applications remain constrained by low enzymatic activity, instability under process conditions, and insufficient understanding of metalloenzyme activation mechanisms. Addressing these challenges, we conducted a genome-driven investigation of 151 salt-tolerant Bacillus strains to identify robust CDAs tailored for industrial demands. Genomic analysis revealed 120 strains harboring CDA genes, with Bacillus pumilus B866 exhibiting the highest native activity (105.93 U/mL). Through systematic medium optimization—identifying lactose, yeast extract, and FeSO₄ as critical components—CDA production in B866 surged to 191.32 U/mL, a 2.39-fold increase over baseline. Heterologous expression of BpCDA in E. coli yielded a recombinant enzyme (123.27 U/mL) with superior thermostability (retaining > 42.9% activity after 24 h at 55 °C) and broad pH adaptability (>81.4% activity at pH 7.0–9.0). Notably, BpCDA demonstrated unique Fe²⁺-dependent activation (186.4% activity enhancement at 1 mM), contrasting with Mg²⁺-dependent systems in prior studies. Comparative genomic and pan-genome analyses underscored evolutionary adaptations linked to saline–alkaline niches, while biosynthetic gene cluster profiling revealed strain-specific metabolic potentials independent of genome size. This study resolves critical limitations in CDA performance by integrating genome mining, targeted screening, and metalloenzyme engineering, establishing a scalable platform for sustainable chitin valorization. The optimized BpCDA, with its industrial-compatible stability and novel activation mechanism, represents a significant advancement toward efficient, eco-friendly chitosan production. Full article

Sweet potato (Ipomoea batatas (L.) Lam.), as an important crop, is rich in polyphenols, vitamins, minerals, and other nutrients in its roots and leaves and is gradually gaining popularity. The use of endophytic bacteria to improve the quality of sweet potato can protect the environment and effectively promote the sustainable development of the sweet potato industry. In this study, 12 strains of endophytic bacteria were isolated from sweet potato. Through nitrogen fixation, phosphorus solubilization, indoleacetic acid production, siderophore production, ACC deaminase production, and carboxymethyl cellulose production, three strains with multiple biological activities were screened out. Among them, MEPW12 had the most plant growth-promoting functions. In addition, MEPW12 promoted host chlorophyll accumulation and inhibited pathogen growth and colonization in sweet potato roots and can utilize various carbon sources and salts for growth. It can also grow in extreme environments of high salt and weak acid. MEPW12 was identified as Bacillus amyloliquefaciens with a genome size of 3,928,046 bp and a GC content of 46.59%. After the annotation of multiple databases, it was found that MEPW12 had multiple enzymatic activities and metabolic potential. Comparative genomics and pan-genomics analyses revealed that other Bacillus sp. strains of MEPW12 have similar functions. However, due to adaptation to different growth environments, there are still genomic differences and changes. Inoculation with MEPW12 induced the high expression of IbGH3.10, IbERF1, and other genes, thereby promoting the growth of sweet potatoes. Bacillus amyloliquefaciens strain MEPW12 is a sweet potato endophyte with multiple growth-promoting functions, which can promote the growth of sweet potato seedlings. This study provides new microbial resources for developing microbial agents and improving the quality of sweet potatoes. Full article

GATA is a crucial transcription factor involved in plant growth, development, and responses to abiotic stress. Therefore, identifying and exploring GATA transcription factors in maize is of significant importance. In this study, we identified 75 ZmGATA genes based on the pan-genome of maize, which includes 26 high-quality maize genomes. These consist of 58 core genes (present in all 26 lines), 12 non-essential genes (present in 2 to 23 lines), 2 near-core genes (present in 24 to 25 lines), and 3 private genes (present in only 1 line). By evaluating the Ka/Ks ratio of the ZmGATA genes in 26 maize varieties, we found that the Ka/Ks ratios of ZmGATA31, ZmGATA32, ZmGATA36, and ZmGATA9 were greater than 1, which may indicate that these four genes are under positive selection. In contrast, the Ka/Ks ratios of other ZmGATA genes were less than 1, suggesting that these genes may be under purifying selection. In the 26 maize genomes, we observed a significant difference in the expression of ZmGATA8 between varieties affected by structural variations (SVs) and those not affected. In certain varieties, SVs altered conserved structures. Additionally, we analyzed the expression levels of ZmGATA genes in different maize tissues and under abiotic stress. ZmGATA38 and ZmGATA39 were highly expressed in the endosperm, thereby influencing starch synthesis, while ZmGATA7, ZmGATA10, ZmGATA19, ZmGATA28, and ZmGATA40 were found to be associated with abiotic stress responses. These findings provide valuable new resources for functional research on ZmGATA. Full article

The abiotic stresses associated with spring/fall freezes and extreme winter cold cause significant economic losses in blueberry production. These problems are exacerbated by climate change and increasingly erratic weather patterns. Developing freeze-tolerant blueberry cultivars with optimized cold hardiness, chilling requirement, and flowering and fruiting phenology holds promise for mitigating the risk of these weather-related damages. These weather-resilient cultivars will ensure the long-term productivity and sustainability of the blueberry industry. The focus of this review is to present the current understanding of the major components of genetic breeding for blueberry freeze tolerance, i.e., phenotyping, genotyping, genetic association analysis, and marker development. The advancement in gene regulation and corresponding proteomic changes upon cold acclimation, dormancy, de-acclamation, and flowering and fruiting aids in the understanding of the adaptive stress response in blueberries. A wide range of genetic diversity in freeze tolerance and phenological traits has been identified among cultivated and wild blueberry relatives. Significant efforts have been made to phenotype freeze tolerance, chilling requirement, and flower and fruit development in both field and controlled environmental conditions. Recent studies emphasize the need for high-throughput, image-based phenotyping of blueberry flower development to improve the precision and efficiency of selecting freeze-resilient genotypes. In addition, advancements in blueberry genomics and pangenome resources expanded the potential of variant calling and high-density linkage map construction. Genetic association studies have identified QTL regions linked to freeze tolerance in blueberries, providing valuable targets for selection. The implementation of these advanced genomic tools and high-throughput phenotyping methodology will accelerate the development of weather-resilient blueberry cultivars. Full article

The strain A-9^T, isolated from Oncorhynchus mykiss (rainbow trout) in a Turkish aquaculture facility, was characterized through integrated phenotypic, phylogenetic, and genomic analyses. Whole-genome sequencing revealed a 5.21 Mb circular chromosome (GC content: 58.16%) and three plasmids encoding proteins for mobilization and toxin–antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9^T. Digital DNA–DNA hybridization (77.6–78.6%) and average nucleotide identity values (96.59–97.58%) confirmed taxonomic divergence from all currently recognized A. salmonicida subspecies. Comparative proteomic and pangenomic analyses identified 328 strain-specific genes, including virulence factors, secretion system components (Type II and Type VI), and efflux-related proteins. Although genes encoding Type III secretion systems and biofilm formation were absent, A-9^T harbored a broad virulence gene repertoire and resistance determinants, including OXA-956, cphA5, and FOX-20, supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon Aeromonas salmonicida subsp. oncorhynchi subsp. nov. (type strain A-9^T = LMG 33538^T = DSM 117494^T), expanding the taxonomic landscape of the A. salmonicida complex and offering insights into fish-associated bacterial evolution. Full article

The rumen microbiome represents a cornerstone of ruminant digestive physiology, orchestrating the anaerobic fermentation of plant biomass into short-chain fatty acids (SCFAs)—critical metabolites underpinning host energy metabolism, immune function, and environmental sustainability. This comprehensive review evaluates the transformative role of pan-genomics in deciphering the genetic and metabolic networks governing SCFA production in the rumen ecosystem. By integrating multi-omics datasets, pan-genomic approaches unveil unprecedented layers of microbial diversity, enabling precise identification of core functional genes and their dynamic contributions to carbohydrate degradation and SCFA biosynthesis. Notable advancements include the following: mechanistic insights into microbial community assembly and metabolic pathway regulation, highlighting strain-specific adaptations to dietary shifts; precision interventions for optimizing feed efficiency, such as rationally designing microbial consortia and screening novel feed additives through pan-genome association studies; and sustainability breakthroughs, demonstrating how targeted modulation of rumen fermentation can simultaneously enhance production efficiency and mitigate methane emissions. This synthesis underscores the potential of pan-genomics to revolutionize ruminant nutrition, offering a blueprint for developing next-generation strategies that reconcile agricultural productivity with environmental stewardship. The translational applications discussed herein position pan-genomics as a critical tool for advancing animal science and fostering a resilient livestock industry. Full article