Search Results (2,080)

Background: Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is increasingly recognized as a multidrug-resistant (MDR) nosocomial pathogen. However, subspecies-level genomic data from Ecuador remain limited. Methods: Four clinical E. hormaechei isolates from a hospital in northern Ecuador were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Genomic characterization included multilocus sequence typing (MLST), resistome profiling, plasmid replicon detection, integron screening, genomic island analysis, and phylogenetic comparison with publicly available Ecuadorian genomes. Results: WGS identified three isolates as subsp. xiangfangensis (ST136 and ST337) and one as subsp. hoffmannii (ST145). Two ST136 isolates exhibited extensive MDR phenotypes associated with bla_CTX-M-15, bla_OXA-1, bla_ACT-16, and additional aminoglycoside and fluoroquinolone resistance genes. ST145 showed moderate resistance, whereas ST337 remained largely susceptible despite harboring bla_ACT-16. Multiple genomic islands and plasmid replicons (IncF/IncR or IncHI2) were detected. Phylogenetic analysis demonstrated clustering with previously reported Ecuadorian lineages. Conclusions: This study provides subspecies-level genomic characterization of clinical E. hormaechei in Ecuador and describes heterogeneous resistance profiles and associated mobile genetic elements, contributing baseline data for regional surveillance. Full article

(1) Background: Potentially arthropod-pathogenic and plant-associated Metarhizium fungi are of high interest for basic research, biological pest control and plant growth promotion. Unambiguous species delineation enabling the taxonomic assignment of new isolates and the identification of new Metarhizium species is of crucial importance for both research and application. Recently, the new species Metarhizium hybridum and Metarhizium parapingshaense were introduced on the basis of phylogenomic studies. (2) Methods: Neighbor- joining and Bayesian inference-based phylogenetic reconstruction of ribosomal intergenic spacer (rIGS) sequences were used to critically evaluate new species introductions. A species-discriminating diagnostic PCR tool for Metarhizium was adapted to M. hybridum and M. parapingshaense. GenBank database mining was performed to identify cryptic descriptions of the new species. (3) Results: The introduction of M. hybridum and M. parapingshaense was corroborated by rIGS sequence comparison. Data mining revealed cryptic first descriptions of M. hybridum from Canada, China, Colombia, Costa Rica, Cuba, Honduras, Mexico, New Zealand, the USA and the Philippines, and of M. parapingshaense from China, India, Japan, the Philippines and South Korea. (4) Conclusions: Results support the reliability of rIGS as a single taxonomic marker for species-level identification of Metarhizium fungi. Species-discriminating diagnostic PCR was successfully adapted to enable the sequencing-independent identification of the confirmed new species M. hybridum and M. parapingshaense. Full article

Background: The genus Brucella has expanded considerably in the 21st century. With the advent of advanced phylogenetic analyses, a close genetic relationship between Brucella and Ochrobactrum has been identified, leading to reclassification of Ochrobactrum species within the genus Brucella. Among these, Brucella anthropi (formerly Ochrobactrum anthropi) is increasingly recognized as a rare cause of invasive human infection. We report a clinically significant case of B. anthropi infective endocarditis and review the available literature. Methods: We report a case of B. anthropi infective endocarditis and conducted a narrative review of the English-language medical literature through 2025. Cases were analyzed for demographics, clinical presentation, antimicrobial susceptibility, and outcomes. Results: A 75-year-old man with a prosthetic aortic valve and prior endocarditis presented with fever of unknown origin, weight loss, and prior transient ischemic attacks. Blood cultures grew B. anthropi after prolonged incubation. Transesophageal echocardiography demonstrated vegetations involving both the aortic and tricuspid valves, and the patient required targeted combination antimicrobial therapy due to persistent bacteremia. Seven additional cases of B. anthropi infective endocarditis were identified on review of the literature. Most patients had underlying valvular disease or prosthetic material. Reported lethality approached 25%. Antimicrobial susceptibility patterns were variable, underscoring the importance of targeted individualized therapy. Conclusion: Consistent with other Gram-negative bacilli, B. anthropi is a rare but established cause of acute bacterial endocarditis. Despite its rarity, it may represent an under-recognized cause of invasive disease. This case highlights the importance of prolonged culture incubation, careful microbiologic interpretation, and susceptibility-guided therapy. Full article

Background/Objectives: Castanopsis tibetana Hance (C. tibetana) is a valuable timber species in southern China. Its chloroplast and nuclear genomes have been characterized, but its mitochondrial genome (mitogenome) remains unknown. This study assembles and characterizes the first complete mitogenome of C. tibetana, elucidating its structural and evolutionary features. Methods: A hybrid approach combining Oxford Nanopore long reads and Illumina short reads was used. The mitogenome was assembled via iterative seed-based mapping and annotated via GeSeq and tRNAscan-SE. Repeats were identified via MISA, TRF, and REPuter. The RNA editing sites were predicted with the PREP suite. Phylogenetic analysis was performed on 14 conserved protein-coding genes from 13 species via maximum likelihood and Bayesian inference. Results: The mitogenome is a 554,078 bp circular molecule (GC 45.27%) encoding 51 genes (32 PCGs, 16 tRNAs, 3 rRNAs). It contains 202 simple sequence repeats (37.1% tetrameric). We predicted 53 C-to-U RNA editing sites, most frequently in nad7 and nad5. Codon usage showed bias, with 28 codons having RSCU > 1. Twenty fragments (6001 bp, 1.08% of the mitogenome) were transferred from the chloroplast. Phylogenomic analysis placed C. tibetana within Fagaceae, close to other Castanopsis species. Conclusions: This study provides the first comprehensive characterization of the C. tibetana mitogenome, revealing its structural architecture, repetitive landscape, RNA editing profile, and phylogenetic placement. These findings offer valuable genomic resources for understanding mitogenome evolution in Fagaceae and support future research on the conservation genetics and molecular breeding of this important tree species. Full article

Background: Chlorophyll degradation is a characteristic sign of fruit ripening. However, the chlorophyll degradation pathway during pitaya fruit development remains unexplored. Methods and Results: Here, chlorophyll contents showed a downward trend across the five developmental stages of ‘Jindu No.1’ pitaya peels. Based on the pitaya genome data, twenty chlorophyll degradation genes were identified, including two NYCs, three CLHs, five SGRs, six PAOs, and four RCCRs, spread across eight pitaya chromosomes. In addition, their phylogenetic relationships, conserved motifs, and domains were analyzed using homologous genes from beet and Arabidopsis species. Transcriptomic data and RT-qPCR analyses of these genes suggested that three HuSGRs demonstrated a significant upward trend during pitaya peel maturation. Indeed, the HuSGR1 has the complete gene structure, including the chloroplast transit peptide, SGR domain, and variable C-terminal region. However, HuSGR2 and HuSGR3 contained the N- and C-terminal sequences, respectively, of HuSGR1. They were separated by a 690 bp distance on chromosome 8, forming a gene cluster. Overexpressed HuSGR2 or HuSGR3 alone resulted in a significant decrease in chlorophyll contents in tobacco leaves. Notably, a more obvious reduction of chlorophyll contents was observed when overexpressing them together. Conclusions: Our results show that HuSGR2 and HuSGR3 were involved in accelerating the chlorophyll degradation process, providing new insights into the molecular basis of color formation in pitaya peels. Full article

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article

Acanthamoeba is a free-living amoeba (FLA) that causes the majority of human infections. It is found predominantly in aquatic environments and is classified according to morphology or genotype (T1-T23). Research on this FLA aims to monitor its distribution, identify existing genotypes, assess its infectious potential, and identify factors that contribute to its recurrence. This study performed a molecular characterisation of Acanthamoeba strains isolated from tap water in Cajeme, Sonora, Mexico, to classify their genotypes. This was complemented by whole-genome sequencing and mapping of the 18S rRNA region in a divergent strain, LUDO1, to obtain higher-resolution data for more reliable assessment of its divergence from known genotypes. Genotypes T4, T5, T11, and T15 were identified in the Acanthamoeba-specific amplimer S1 (ASA.S1) region using the maximum-likelihood method. The inclusion of the 18S rRNA region from strain LUDO1 enabled its classification as a new genotype (T24), with a dissimilarity exceeding 5% compared with the 23 known genotypes. Additionally, culture analysis revealed notable variation in trophozoite size among strains that correlated with phylogenetic sub-branching. This analysis contributed to the epidemiological understanding of Acanthamoeba’s high resistance to treatments and infection systems and demonstrated a broadening of the phylogenetic distribution within the genus. Full article

Tick-borne encephalitis virus (TBEV) is primarily transmitted by Ixodes spp. and poses significant health risks, leading to morbidity and mortality in humans. Two of the five subtypes, Siberian and Far Eastern are known to circulate in Mongolia. In 2021, Ixodes persulcatus ticks were collected from Bulgan aimag (province) using flagging and dragging methods and subsequently screened for TBEV using PCR. Positive samples underwent sequencing using an Oxford Nanopore Technologies-based hybrid capture approach, resulting in two coding-complete TBEV genomes from separate tick pools. Phylogenetic analysis classified both genomes within the Siberian subtype, grouping them with other Mongolian sequences from I. persulcatus collected in 2014, 2020, 2021, and 2023. The study sequences, PX654173 and PX654174, showed high genetic similarity (99.9% and 99.8%, respectively) to the sequence PQ479142, obtained from I. persulcatus ticks in Selenge, Mongolia, in 2021. The estimated time to most recent common ancestor (TMRCA) of the Siberian genotype was approximately 981 CE (95% HPD: 646–1347) with the emergence of a distinct Mongolian clade of TBEV around 1888 CE (95% HPD: 1834–1934). These findings highlight the value of expanded whole-genome sequencing to improve our understanding of TBEV’s genetic diversity and evolutionary history in Central Asia. Full article

Background/Objectives: To establish a foundation for conserving and utilizing local frog germplasm resources in Zhejiang Province, for Quasipaa spinose, which has high commercial and nutritional value, a pan-genome analysis was performed. Methods: Herein, we characterized 405,263 SNPs for the giant spiny frog, Q. spinose, using the Illumina NovaSeq platform. Results: These loci were highly polymorphic in 59 individuals sampled from three different subpopulations, with 0.05 to 0.30 minor alleles per locus. The observed and expected heterozygosities were 0.2379 and 0.2683 (IBD), respectively. These polymorphic loci would be useful for assessing genetic diversity, population structure, gene flow, population assignment, and paternity in giant spiny frogs. Conclusions: Our investigation demonstrated that there are distinct genetic and evolutionary histories between Zhejiang and Jiangxi frogs. Phylogenetic inference effectively differentiated these three subpopulations based on their geographical origins, and the phylogenetic inference level of domesticated Zhejiang frogs was comparatively higher than that of the Jiangxi-derived population. Furthermore, by utilizing three selective signature methods, namely, Obs/Exp het, nucleotide diversity (Pi), and identical by state (IBS), across subpopulations, we concluded that these three breeds were from an identical population, and no genetic bottleneck occurred among these three lineages, in accordance with LD decay analysis. Finally, 2700 potential candidate genes were identified, including MAPK, calcium signaling pathway, Ras signaling pathway and regulation of actin cytoskeleton; we noted that the key genes associated with dilated cardiomyopathy or arrhythmogenic right ventricular cardiomyopathy in humans beings and GnRH signaling pathway-related genes (i.e., CD80, IFNA, and KCNK1) were highly enriched, which could impact cardiac function through immune-associated genes. Full article

Background/Objectives: Non-indigenous species are increasingly reshaping Mediterranean marine ecosystems, particularly under ongoing climate warming. The rayed pearl oyster Pinctada radiata, a thermophilic species originating from the Indo-Pacific region, is one of the earliest and most successful invaders in the Mediterranean Sea and has recently established populations in the Adriatic Sea. Methods: This study integrates preliminary shell morphometric data with molecular genetic analyses based on mitochondrial cytochrome c oxidase subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) markers to confirm species identity and examine patterns of genetic variation in comparison with other Mediterranean Sea regions and the Persian Gulf. Results: Phylogenetic analyses based on COI confirmed P. radiata as a distinct and well-supported monophyletic lineage, whereas the nuclear ITS2 marker showed limited resolution and interspecific overlap. Mediterranean and Adriatic populations showed low COI haplotype and nucleotide diversity and weak genetic structuring, consistent with recent colonization and secondary expansion, whereas Persian Gulf populations were more genetically diverse. Conclusions: Future studies should employ larger sample sizes and broader geographic sampling across both the Mediterranean Sea and the full native range of P. radiata, combined with high-resolution genome-wide nuclear markers, to better resolve connectivity and invasion dynamics. Full article

Background: Sulfate transporters (SULTRs) are integral membrane proteins responsible for sulfate uptake, translocation, and plant adaptation to abiotic stresses. However, knowledge regarding the SULTR gene family in the economically important crop, Brassica rapa (Chinese cabbage), limited. The aim of this study is to conduct a genome-wide identification and functional characterization of BrSULTR genes and to explore their potential functions under abiotic stress. Methods: We identified 19 BrSULTR genes in the B. rapa genome by performing homology searches with Arabidopsis thaliana SULTR sequences as queries. Subsequent bioinformatics analysis included phylogenetic classification, chromosomal localization, gene structure, conserved motif dissection, cis-regulatory element prediction, and protein–protein interaction (PPI) network analysis. Tissue-specific expression profiles of BrSULTRs were assessed using publicly available transcriptome data. Furthermore, their expression dynamics under salt (150 mM NaCl) and low-temperature (4 °C) stress were investigated by integrating transcriptomic, proteomic, and qRT-PCR data. Results: The 19 identified BrSULTR members were phylogenetically categorized into four subfamilies and were mapped unevenly across seven chromosomes. Promoter analysis identified an array of cis-regulatory elements associated with development, hormone response, and stress response. Expression profiles revealed distinct tissue-specific patterns in roots, stems, leaves, flowers, and siliques. Under salt stress, BrSULTR13 was significantly upregulated, while BrSULTR9 and BrSULTR11 were significantly suppressed under low-temperature stress. PPI network projection indicated that the Arabidopsis homologs of BrSULTR5 may physically interact with stress-regulating enzymes such as APS and APR. Conclusions: Our work presents a comprehensive genomic and functional overview of the BrSULTR gene family in B. rapa. The results underscore the potential functions of BrSULTRs, highlighting their involvement in sulfate transport and abiotic stress responses. These insights establish valuable insights and a foundation for further research aiming at improving stress tolerance in B. rapa through the manipulation of sulfur metabolism pathways. Full article

Background/Objectives: The coordination of flowering and dormancy represents a fundamental adaptive strategy for perennial plant survival. Recent studies have demonstrated that AIL1 homologs act as integrators of short-day signals, playing pivotal roles in seasonal growth cessation and dormancy regulation in poplar. Despite these advances, whether AIL1-mediated regulatory mechanisms are conserved in Platanus acerifolia, a species with distinct phylogenetic and ecological characteristics, remains an open question. Methods: In this study, two AIL1 homologs, PaAIL1a and PaAIL1b, were isolated from P. acerifolia. Their biological functions were systematically investigated through sequence analysis, spatiotemporal expression profiling, environmental stress treatments, yeast one-hybrid assays, and luciferase (LUC) transient expression assays. Results: PaAIL1s (PaAIL1a and PaAIL1b) exhibited ubiquitous expression across diverse tissues and organs, functioning as mediators of photoperiod and temperature signaling to orchestrate bud dormancy regulation. Interaction and activation assays placed these factors downstream of PaFUL proteins. While displaying functional redundancy in dormancy induction and floral development, the paralogs underwent distinct subfunctionalization: PaAIL1a specifically regulated flowering initiation and dormancy release, whereas PaAIL1b acted predominantly during the ecodormancy phase. Conclusions: These results establish PaAIL1 genes as critical integrators of environmental signals and developmental programs, governing seasonal growth dynamics in this species. Full article

Background: Uropathogenic Escherichia coli (UPEC) is the primary etiological agent of urinary tract infections (UTIs) worldwide. The emergence of strains combining high virulence with multidrug resistance (MDR) poses a significant challenge to public health. This study aimed to characterize the phylogenetic distribution, virulence profiles, and antimicrobial susceptibility of UPEC isolates recovered from patients in the metropolitan area of Buenos Aires (AMBA), Argentina. Methodology: Phylogenetic groups, the ST131 lineage, and virulence-associated genes were identified using PCR-based assays. Antimicrobial susceptibility testing (AST) was performed using automated methods and extended-spectrum beta-lactamase (ESBL) production was confirmed using the double-disk synergy test. Colistin (COL) resistance was evaluated by Colistin Drop Test and PCR screening for the mcr-1 (mobile colistin resistance gene 1). Biofilm formation was detected by the Tissue Culture Plate (TCP) method, whereas phenotypic virulence factors (VF) were assessed with Congo Red agar, hemagglutination, and hemolysis assays. Results: Phylogenetic groups B2 (43.8%) and D (26.7%), typically associated with extraintestinal infections, were the most frequent. The high-risk clone B2-ST131 was detected in 6.7% of isolates. Biofilm production was observed in 92.4% of the isolates, with curli fimbriae (87.6%) being the most frequently expressed VF. The highest resistance rates were observed for ampicillin (62.1%), ampicillin-sulbactam (39.8%), and trimethoprim-sulfamethoxazole (25.2%). Interestingly, 3.8% of isolates exhibited colistin resistance, despite the absence of the mcr-1 gene. Conclusions: This study highlights the detection of MDR-UPEC isolates that showed strong resistance to fluoroquinolones and were ESBL producers with high virulence in Argentina, justifying future research encompassing genomic and epidemiological monitoring of local UPEC, which is essential for managing infections and developing new therapeutic and preventive measures. Full article

Background: The WRKY transcription factor family represents one of the most crucial transcription factor families in plants, regulating diverse physiological processes. The heartwood of Dalbergia odorifera is a prized material for both high-quality rosewood and traditional medicinal applications, exhibiting exceptional economic value. However, the roles of WRKY transcription factors in the growth and development of D. odorifera, particularly their correlation with heartwood formation, remain unexplored. Methods: WRKY transcription factors were identified through bioinformatics analysis using the published genome data of D. odorifera. Phylogenetic comparative analysis was performed based on the Arabidopsis classification system. Collinearity analysis was conducted to investigate the evolutionary dynamics and expansion mechanisms of the WRKY gene family, and differential expression analysis was performed across tissues. Results: A total of 94 WRKY genes were unevenly distributed across 10 chromosomes and systematically designated as DodWRKY1 to DodWRKY94 according to their chromosomal positions. The WRKY family was classified into three major clades (Groups I, II, and III), with Group II further subdivided into five subgroups (IIa–IIe). Purifying selection served as the primary force shaping the WRKY family, with whole-genome or segmental duplication acting as the dominant expansion mechanism; these duplication events contributed to functional divergence, whereas genes within the same subgroup retained conserved structural features and motif compositions. DodWRKY14 (subgroup IIb) and DodWRKY58/68 (subgroup IIc) were highly expressed in the transition zone, suggesting a potential involvement in heartwood formation. Conclusions: This study provides a comprehensive characterization of the DodWRKY family and identifies candidate genes associated with heartwood formation, thereby establishing a foundation for further investigation into the molecular mechanisms underlying heartwood development. Full article

Background/Objectives: Antimicrobial agents have revolutionized disease management in humans and animals; however, their misuse and overuse have accelerated the emergence and spread of antimicrobial resistance (AMR) and antimicrobial resistance genes (ARGs). Dairy farms are recognized as potential hotspots for ARG dissemination, particularly through Escherichia coli, which acts as a reservoir and vector of ARGs, enabling their horizontal transfer via plasmids and other mobile genetic elements. This study aimed to characterize the genomic diversity, ARG profiles, plasmid content, and phylogenetic relationships of E. coli isolated from dairy farm environments and milk using whole-genome sequencing. Methods: A total of 31 E. coli isolates recovered from soil, effluent, cow dung, and milk samples underwent deoxyribonucleic acid extraction, library preparation, and sequencing on the Illumina MiSeq platform, followed by comprehensive bioinformatic analysis. Results: The E. coli isolates exhibited 20 distinct sequence types, including one novel sequence type. Plasmids were detected in 71% of the isolates, with the IncF plasmid family being the most predominant. Furthermore, 12 ARG groups were identified, with β-lactam resistance genes detected in 67.7% of isolates. Notably, blaCTX-M genes were identified in all phenotypically confirmed extended-spectrum β-lactamase-producing isolates. Additional ARGs, including those conferring resistance to tetracyclines (tet(A), tetX4), quinolones (qnrS1), aminoglycosides (aph, aad, ant), and folate pathway inhibitors (dfr and sul), were widely distributed throughout the samples. Phylogenetic analysis revealed clustering of isolates from different sample types, particularly among ST58 isolates, suggesting cross-environmental transmission. Conclusions: This study demonstrates that E. coli from dairy farm environments harbor diverse ARGs and plasmids, confirming their role as reservoirs of AMR. These findings underscore the importance of prudent antimicrobial use, routine genomic surveillance, and enhanced biosecurity measures to limit cross-environmental transmission. Full article