Search Results (443)

Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D^pol RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D^po region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants. Full article

The aim of this research was to characterize the genetic structure of brown trout species complex populations in nine river basins in the Aosta Valley and neighbouring regions in northern Italy. We used a combined analysis of nuclear lactate dehydrogenase (LDH-C1*), mitochondrial DNA-CR (control region) (mtDNA-CR) sequences and ddRAD-seq-generated single-nucleotide polymorphism. In this way, we estimated the degree of hybridization of wild populations with the Atlantic-derived hatchery lineage. The results of the genetic analyses showed a complex genetic structure with different levels of introgression at the respective sampling sites. The mitochondrial lineages (Atlantic (AT), Mediterranean (ME), Adriatic (AD), and Marmoratus (MA)) were present with varying percentages across the sampling sites. Data analysis using the Admixture v.1.3.0 software allowed the identification of four distinctive cluster units in the Aosta Valley. For the Vertosan River, we identified a distinct native population and a level of hybridization close to zero. In terms of conservation, this population with a distinct native lineage represents a high priority for protection and serves as a reservoir for the entire western north Italian alpine zone. Some interventions to support conservation actions within the study area can be envisaged. Full article

Background: Fluoroquinolone (FQ) resistance in Escherichia coli (E. coli) undermines empiric therapy and often coincides with multidrug resistance (MDR). Because sequencing is not routinely available in many laboratories, we evaluated a phenotype-first, sequencing-independent diagnostic framework deployable on standard platforms. Methods: We profiled 45 archived E. coli isolates for susceptibility (Clinical and Laboratory Standards Institute [CLSI]-guided), extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase (AmpC) phenotypes, MDR, and multiple-antibiotic resistance (MAR) indices. Ten founders (five FQ-susceptible [FQ-S], five low-level resistant [LLR]) seeded 20 parallel lineages exposed to stepwise ciprofloxacin. We tracked minimum inhibitory concentrations (MICs), collateral resistance, growth kinetics, and biofilm biomass using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification, automated and reference antimicrobial susceptibility testing (AST), growth-curve analysis, and crystal violet microtiter assays. The intended use is a sequencing-independent workflow for routine laboratories—especially where whole-genome sequencing is not readily available—working with archived or prospective clinical E. coli. This workflow is best applied when local FQ nonsusceptibility threatens empiric reliability; inputs include standard ID/AST with simple growth and biofilm assays. Primary outputs include: (i) MIC trajectories with time to high-level resistance (HLR), (ii) ΔMAR-summarized collateral resistance with class-level susceptible-to-resistant conversions, and (iii) concise fitness/biofilm summaries to guide empiric-policy refresh and early de-escalation. Results: At baseline, ciprofloxacin nonsusceptibility was 40.0%; ESBL and AmpC phenotypes were confirmed in 28.9% and 15.6%, respectively; 46.7% met the MDR definition; and the median MAR index was 0.29. During evolution, 70% of lineages reached HLR (MIC ≥ 4 μg/mL), with earlier conversion from LLR versus FQ-S founders (median 7 vs. 11 passages). Collateral resistance emerged most often to third-generation cephalosporins (3GCs), trimethoprim–sulfamethoxazole, and tetracyclines, while carbapenem activity was preserved. MAR increased in parallel with rising MICs. Resistance acquisition imposed modest fitness costs (slightly reduced growth rates and longer lag phases) that were partly offset under subinhibitory ciprofloxacin, whereas biofilm biomass changed little. Conclusions: this phenotype-first, routine-laboratory workflow rapidly maps FQ resistance and clinically relevant co-selection in E. coli. In high-resistance settings, empiric FQ use is difficult to justify, and MAR trends provide practical co-selection signals for stewardship. This reproducible framework complements genomic surveillance and is directly applicable where sequencing is unavailable. Full article

Background: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a genetically distinct lineage from healthcare-associated MRSA (HA-MRSA), often producing Panton-Valentine leukocidin (PVL) and causing severe skin and soft tissue infections (SSTIs) in otherwise healthy individuals. Methods: We describe five cases of PVL-positive CA-MRSA SSTIs admitted to the Infectious Diseases Unit of the University Hospital “Paolo Giaccone,” Palermo, Italy, between 2024 and 2025. Case inclusion followed the CDC criteria for CA-MRSA. Microbiological identification was performed using MALDI-TOF mass spectrometry, and antimicrobial susceptibility testing followed EUCAST standards. PVL gene presence was confirmed by polymerase chain reaction. Results: Clinical management included surgical drainage, systemic antibiotic therapy, and decolonization of both patients and close contacts. Long-acting lipoglycopeptides (oritavancin or dalbavancin) were evaluated as therapeutic options to achieve clinical resolution. Conclusions: PVL-positive CA-MRSA infections are characterized by recurrence, intrafamilial clustering, and frequent therapeutic failure with standard oral agents. Effective management requires an integrated approach combining prompt surgical drainage; systemic therapy, preferably including long-acting lipoglycopeptides; and comprehensive decolonization of all close contacts. Full article

This study aimed to characterize Mycoplasmosis bovis strain 16M—a highly virulent isolate from one Chinese outbreak—as a candidate for challenge models and inactivated vaccine development. We assessed strain 16M through morphological observation, PCR identification, drug susceptibility testing, growth titer and biofilm quantification, immunological profiling, and calf challenge experiments. We used genomic resequencing to evaluate the genetic stability across 150 passages. Classified as the prevalent ST52 lineage in China, strain 16M showed phylogenetic proximity to strain 08M and exhibited multidrug resistance (notably to macrolides). It achieved higher titers and stronger biofilm formation than other isolates and the reference strain PG45. In calves, intratracheal inoculation with 16M induced universal infection, severe pulmonary consolidation, and peribronchial cuffing, with significantly higher disease scores (p < 0.01). The inactivated 16M vaccine elicited elevated antigen-specific IgG titers, PBMC proliferation, and IFN-γ production versus PG45. Post challenge, immunized calves showed reduced pathological lesions, shorter bacterial shedding, and lower disease scores than the infected controls (p < 0.05). Genetic stability was confirmed for virulence-associated genes (e.g., adhesion proteins), with stable titers and biofilm production within 50 generations. Strain 16M combines high virulence for challenge modeling and industrial-scale vaccine suitability, owing to its robust growth, stable immunogenicity, and genetic consistency. Full article

Plant-based meat (PBM) products have rapidly grown in popularity due to increasing consumer demand for sustainable, ethical, and health-oriented food alternatives. However, these novel products may pose microbiological risks similar to traditional meats, including contamination by Salmonella spp. In this study, PBM samples (n = 63), including raw products (ground pork, mushroom, and burger) and cooked products (chicken tender, chicken breast, nugget, and beef), were collected from local retail markets in Bangkok, Thailand. The prevalence of Salmonella spp. was assessed by calculating the proportion of confirmed positive samples relative to the total number of PBM products tested. Additionally, the genomic characteristics and antibiotic susceptibility of Salmonella isolated from PBM were also investigated. From the result, Salmonella enterica was detected in 2.44% (1/41) of raw PBM samples, whereas no contamination was observed in cooked PBM products (0/22). Serovar identification revealed the isolate to be S. Anatum. Whole genome sequencing (WGS) analysis revealed the genome of S. Anatum SPBM3 consisted of 4,726,256 base pairs with 52.15% GC content, encoding 4717 coding sequences (CDS). Pangenomic analyses placed S. Anatum SPBM3 within a distinct sub-cluster closely related to pathogenic Salmonella strains previously reported, confirming its identity as part of the S. enterica lineage. The genome harbored 67 antimicrobial resistance genes, 5 prophage elements, and 305 key virulence determinants. Phenotypically, the isolate exhibited susceptibility to most tested antibiotics but showed intermediate resistance to streptomycin, ciprofloxacin, and colistin. Our findings highlight the potential microbial risks associated with PBM products and emphasize the importance of genomic surveillance to ensure food safety and public health protection as dietary preferences evolve toward non-traditional food matrices. Full article

Background: Thrushes (family Turdidae) are ecologically important passerine birds widely distributed across the Northern Hemisphere. However, the phylogenetic placement of several East Asian congeners, including Turdus pallidus, remains insufficiently resolved due to the limited resolution of partial mitochondrial or nuclear markers used in previous studies. Methods: In this work, we sequenced and annotated the complete mitochondrial genome of T. pallidus (16,739 bp) using high-throughput Illumina sequencing. The mitogenome exhibited the typical circular architecture and contained 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), with an overall GC content of 47.32%. Results: Most protein-coding genes initiated with the standard ATG codon, although lineage-specific deviations such as GTG in COX1 and ND2 were identified, and incomplete stop codons (T– or TA–) were observed, consistent with post-transcriptional polyadenylation. The 22 tRNA genes displayed typical cloverleaf secondary structures, except for trnS(AGN), which lacked a DHU arm, while rRNA genes were 977 bp (12S, 48.52% GC) and 1590 bp (16S, 44.65% GC), showing conserved stem regions but variable loop regions. Codon usage analysis revealed a strong bias toward A/T-ending codons, with a total of 3798 codons and an effective number of codons (ENC) of ~40, indicating moderate codon bias shaped by both mutational pressure and translational selection. Comparative analysis of evolutionary rates demonstrated that conserved genes such as COX1 and CYTB are suitable for resolving deeper relationships, whereas rapidly evolving genes like ATP8 provide resolution among closely related taxa. Conclusions: Phylogenetic reconstructions based on 13 mitochondrial protein-coding genes robustly supported the monophyly of Turdidae and recovered T. pallidus as most closely related to T. obscurus. Overall, this study provides a novel mitogenomic resource for T. pallidus, enhances phylogenetic resolution within Turdus, and underscores the value of complete mitochondrial genomes for molecular identification, conservation management, and avian evolutionary studies. Full article

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

YABBY belongs to the family of plant-specific transcription factors, known for their role in plant morphology, growth, and development. Its name is derived from the first discovered member—the YABBY1 gene of Arabidopsis thaliana (named due to its mutated phenotype showing a “Y-shaped” bifurcation). Despite extensive research across various plant species, no studies have conducted a genome-wide investigation of the YABBY gene family in Cerasus humilis. This study identified six ChYABBY (Cerasus humilis YABBY) genes distributed across five chromosomes through a comprehensive bioinformatic analysis of the C. humilis genome. The gene expression during the four growth phases was confirmed using real-time-quantitative fluorescent PCR (qPCR). ChYABBY is segmented into five distinct subfamilies. Genetic lineage analysis determined the close genetic relationship between the YABBY genes of C. humilis and Malus pumila. An examination of the gene architecture and preserved motifs revealed that ChYABBY typically comprises 5–6 introns, with motif1, motif2, and motif3 being preserved domains across all ChYABBY protein sequences. Promoter analysis suggests that ChYABBY genes play various roles in the growth and maturation of C. humilis. An examination of the homology revealed the absence of tandem replication in the ChYABBY gene family, with a single pair of fragment-replicating genes. The heat map and q-PCR results indicate that the expression of the ChYABBY gene is tissue-specific and correlates with some aspects of the fruit growth and development. This suggests a potential role for this gene family in fruit maturation. The determination of total sugar and total flavonoid content indicated that the content of the two substances was high when the fruit was green. The antioxidant capacity of the fruit at each stage was different. This research provides an important basis for further understanding the structure and function of the ChYABBY gene, and lays a foundation for the identification of YABBY genes in Rosaceae plants. Full article

RNA editing is a crucial mechanism regulating gene expression in plant organellar genomes, which optimizes protein structures through base substitution and plays a vital role in plant growth, development, and stress adaptation. This study revises the conventional understanding restricting MORF proteins to seed plants by reporting their first identification in ferns, an early vascular plant lineage. We sequenced chloroplast genomes of O. japonica and P. vachellii, revealing one MORF9 homolog in O. japonica and three homologs (MORF1/8/9) in P. vachellii through comparative transcriptomics and structural validation. All identified MORF proteins harbor conserved MORF-box domains, suggesting structural and potentially functional conservation with angiosperms. Crucially, MORF members differentially regulate organellar RNA editing: chloroplast editing frequencies are predicted to show dose-dependent enhancement (0.7–1.0 in conserved sites), potentially influenced by MORF presence or copy number. In O. japonica, chloroplast editing exhibits tissue-specific patterns (conserved sites 0.7–1.0; tissue-specific sites lower efficiency at 0.1–0.2), while this study’s mitochondrial editing results show a balanced frequency distribution (0–1 range). Amino acid substitution analysis demonstrates MORF-mediated hydrophobic optimization (Ser→Leu > 30%, Pro→Leu > 18%), likely underpinning fern adaptability. This work provides crucial initial evidence for a conserved MORF-mediated RNA editing module shared between these early vascular plants (ferns) and angiosperms, offering fundamental insights into the evolutionary trajectory of plant organellar gene regulation. Full article

Capsicum annuum (pepper) is a globally significant Solanaceous crop vulnerable to devastating pathogens such as Phytophthora capsici. Nucleotide-binding leucine-rich repeat (NLRs) proteins are crucial intracellular immune receptors mediating effector-triggered immunity (ETI). This study presents the comprehensive genome-wide identification and analysis of the NLR gene family in pepper using the high-quality ‘Zhangshugang’ reference genome. We identified 288 high-confidence canonical NLR genes. Chromosomal distribution analysis showed significant clustering, particularly near telomeric regions, with Chr09 harboring the highest density (63 NLRs). Evolutionary analysis demonstrated that tandem duplication is the primary driver of NLR family expansion, accounting for 18.4% of NLR genes (53/288), predominantly on Chr08 and Chr09. Analysis of promoter cis-regulatory elements (CREs) revealed enrichment in defense-related motifs, with 82.6% of promoters (238 genes) containing binding sites for salicylic acid (SA) and/or jasmonic acid (JA) signaling. Transcriptome profiling of Phytophthora capsici-infected resistant (C. annuum cv. CM334) and susceptible (C. annuum cv. NMCA10399) cultivars identified 44 significantly differentially expressed NLR genes, and protein–protein interaction (PPI) network analysis predicted key interactions among them, with Caz01g22900 and Caz09g03820 as potential hubs. This study elucidates the tandem-duplication-driven expansion, domain-specific functional implications, and expression dynamics of the pepper NLR family. It identifies conserved and lineage-specific candidate NLR genes, including Caz03g40070, Caz09g03770, Caz10g20900, and Caz10g21150. These findings provide valuable candidate gene targets for the development of molecular markers for pepper resistance to Phytophthora capsici. Full article

Background/Objectives: In this study, we conducted molecular identification of R.microplus and explored the genetic diversity of R. microplus for the first time in Mizoram, a Northeastern Hill (NEH) state of India bordering Myanmar. Methods: To assess genetic variation and evolutionary relationships, we employed phylogenetic analyses, genetic divergence metrics, and haplotype network construction based on mitochondrial (COX1 and 16S rDNA) and nuclear (ITS-2 and 18S rDNA) markers. Additionally, multivariate Principal Coordinate Analysis (PCoA) was used to visualize genetic differentiation among R. microplus populations. Results: Our analyses indicated that populations of R. microplus sensu lato from India, Bangladesh, and Pakistan form a closely related matrilineal lineage distinct from R. microplus sensu stricto, clustering within clade C of the COX1-based phylogeny. Globally, 24 COX1 haplotypes were recovered, with 1 haplotype identified in India. The Mizoram population exhibited a single 16S rDNA haplotype; however, intraspecific divergence was evident across India, with seven matrilineal haplotypes detected and nineteen globally. Further, five haplotypes were identified within R. microplus using the ITS-2 marker, while five haplotypes were observed within the Rhipicephalus genus using the 18S rDNA marker. Moreover, this study revealed the presence of Coxiella-like endosymbionts in 95% of the tick specimens analyzed. Conclusions: This study fills a critical knowledge gap by providing the first molecular documentation of tick diversity in Mizoram, a strategic region along the Indo–Myanmar border, and offers novel insights into the phylogeography and symbiotic associations of R. microplus and related tick taxa. Full article

Congenital hearing loss, frequently resulting from defective hair cells, remains poorly understood due to the incomplete identification of key pathogenic genes. Oncomodulin (OCM) is a kind of calcium-binding protein (CaBP) that regulates diverse cellular processes and is thought to play crucial roles in auditory function. In teleost fish, parvalbumin 8 (pvalb8) and parvalbumin 9 (pvalb9) belong to the oncomodulin lineage and are highly expressed in hair cells. In this study, we first reported the oncomodulin lineage function in fish and identified pvalb8 as an essential regulator of hair cell development. Single-cell RNA sequencing (scRNA-seq) and whole-mount in situ hybridization (WISH) revealed that pvalb8 is highly and specifically expressed in supporting cells and hair cells. Functional loss of pvalb8, achieved via CRISPR/Cas9 knockout or morpholino knockdown, resulted in reduced neuromast size and a significant decrease in neuromast hair cell number, leading to auditory behavioral deficits. In addition, pvalb9 mutants exhibited hair cell defects similar to those observed in pvalb8 mutants, including a significant reduction in hair cell number. Moreover, pvalb8 loss strongly inhibited the proliferation of supporting cells, which likely accounts for the reduced number of differentiated hair cells. The expression levels of Wnt target genes, axin2, ccnd1, and myca, were all significantly reduced in pvalb8 mutants compared to control zebrafish, while activation of the Wnt signaling pathway rescued the hair cell loss observed in pvalb8 mutants, indicating that pvalb8 promotes hair cell development via Wnt-dependent proliferative signaling. These findings highlight pvalb8 as a critical factor in the regulation of auditory hair cell formation and function in zebrafish, offering new insights into the role of oncomodulin lineage in sensory cell development. Full article

Universal Stress Protein (USP) plays crucial roles in plant stress adaptation, yet their evolutionary dynamics, regulatory mechanisms, and functional diversification in rice (Oryza sativa) remain poorly understood. This study aimed to conduct a genome-wide identification and characterization of the OsUSP gene family to elucidate its role in abiotic stress responses using integrated bioinformatics approaches. Here, we identified 46 OsUSP genes that are unevenly distributed across 11 rice chromosomes and exhibit significant divergence in protein length, molecular weight, and subcellular localization. Phylogenetic analysis classified OsUSPs into three subfamilies, with conserved motif and domain architectures within groups but distinct structural variations across subfamilies. Evolutionary analysis revealed strong collinearity between rice and other monocots, which suggests functional conservation in grasses, whereas limited synteny with dicots indicates lineage-specific divergence. Cis-regulatory element analysis showed enrichment in ABA, MeJA, drought, and hypoxia response motifs, implicating OsUSPs in hormonal and stress signaling. Expression profiling indicated tissue-specific patterns, with subfamily III genes broadly expressed, while subfamily II members were anther-enriched. Stress response profiling revealed that 24 OsUSPs were significantly induced, while LOC_Os02g54590 and LOC_Os05g37970 emerged as particularly notable due to their broad-spectrum responsiveness, being upregulated under all tested stress conditions. Protein–protein interaction (PPI) analysis indicated that OsUSP proteins potentially interact with Leo1/TPR-domain proteins and are involved in stress response and phosphorylation signaling pathways. This study yields key insights into OsUSP-mediated stress adaptation in rice and pinpoints promising candidate genes to facilitate the breeding of climate-resilient rice. Full article

Cannabis sativa L. (2n = 2x = 20) is a widely recognized species within the Cannabaceae family. Despite its utilization for medicinal, recreational, and industrial purposes, alongside its extensive historical background, the number of genetic and biotechnological studies of this plant species has decreased due to legal ramifications and prohibition campaigns associated with its use and cultivation. For many years, the development of novel varieties has been pursued solely by cultivators, as domestic growers have transitioned their work from cultivation to breeding Cannabis lineages. Recently, the application of genomics has facilitated a surge in methodologies aimed at marker-assisted selection, germplasm management, genetic differentiation, authentication of cultivated varieties or cultivars, and forensic applications such as safeguarding intellectual property rights. Nevertheless, the utilization of molecular markers for the advancement of commercial varieties through marker-assisted breeding (MAB) frameworks remains rare. This investigation was designed to evaluate a previously established informative microsatellite (SSR) array for the genotyping of drug-type Cannabis sativa cultivars derived from seeds of European origin. A total of 171 samples from 20 varieties were collected from European distributors and analyzed for genetic uniformity and population structure. The results were then compared with previously analyzed hemp samples and drug-type samples of Canadian origin, revealing the identification capabilities of our SSR genotyping method. Full article