Search Results (5,238)

Wild orchid populations are declining with intensified habitat fragmentation posing severe challenges to germplasm conservation. As an important ornamental Orchidaceae species, Cymbidium ensifolium has abundant germplasm resources and frequent natural and artificial hybridization. Long-term natural evolution and anthropogenic disturbance have led to complex genetic backgrounds and ambiguous phylogenetic relationships hindering accurate germplasm identification, elite resource excavation, and selective breeding. As a distinctive variety, Cymbidium ensifolium var. susin has great breeding potential. Clarifying its phenotypic and genetic characteristics is crucial for accelerating breeding progress. In this study, phenotypic determination, Hyper-seq reduced-representation genome sequencing, SNP/InDel genotyping, genetic diversity analysis, and core collection construction were used to evaluate the genetic diversity, population differentiation, and core germplasm screening of 13 Cymbidium ensifolium var. susin accessions. The results showed significant phenotypic differences and rich genetic variation among tested materials. Based on highly weighted floral traits, accessions were divided into three major phenotypic groups. At the molecular level, 963,239 SNP and 182,399 InDel loci were identified and mainly distributed in intergenic regions, followed by introns and exons. A phylogenetic tree was constructed from SNP loci combined with principal component and phenotypic clustering analyses. This study preliminarily clarified the genetic structure of pure-heart Cymbidium ensifolium var. susin, showing a distinct geographical pattern: “high consistency in Fujian and Guangdong; strong differentiation in Southwest China; and a transitional gradient in Central China”. Meanwhile, six core germplasm accessions were screened in this study, which provides a solid theoretical basis and material support for the conservation of pure-heart Cymbidium ensifolium var. susin accessions, variety improvement, hybrid parent selection, and molecular marker-assisted breeding. This is of great significance for promoting the innovation of Chinese orchid germplasm resources and the high-quality development of the industry. Full article

Potato early blight (EB), caused by Alternaria, is an economically devastating fungal disease affecting global potato production. Using a hybrid population derived from distantly related varieties, we combined resistance evaluation, histological analysis, Bulked Segregant Analysis sequencing, RNA sequencing and molecular dynamics simulation, which successfully identified key candidate resistance genes. Genetic mapping localized three major resistance-associated regions on chromosome 8 spanning positions 25.07–29.20 Mb, 38.05–38.80 Mb, and 39.40–40.78 Mb. Through candidate gene analysis, we identified CND41, encoding an aspartic protease, as the prime candidate. This gene exhibited significantly higher basal expression levels and stronger pathogen-induced upregulation in resistant genotypes. Molecular dynamics simulations further identified six crucial non-synonymous mutations in the TAXI-N domain that likely contribute to enhanced resistance by destabilizing the susceptibility-associated protein conformation. Transient overexpression of CND41 provided functional evidence supporting its likely involvement in early blight resistance (EBR). These findings contribute valuable genetic resources and a strong candidate gene for molecular breeding toward EBR potato varieties. Full article

The 2022 highly pathogenic avian influenza (HPAI) outbreak of H5N1 clade 2.3.4.4b was one of the major avian influenza outbreaks, leading to multiple spillover events infecting domestic and wild bird flocks, as well as mammals. The sustained spread was a result of viral circulation in wild birds across migratory flyways in North America. Pennsylvania has a significant poultry population that supports both retail and live bird markets. The state also features migratory bird stopovers on the Atlantic flyway, increasing exposure to HPAI infections. This study investigates clinical presentation and sequence data from H5N1 clade 2.3.4.4b viruses during the 2022 outbreak in Pennsylvania. Eight different H5N1 clade 2.3.4.4b genotypes were detected (A1, B1.1, B1.2, B1.3, B2.2, B3.3, B3.5, and one minor genotype) during the first year. The earliest detection was genotype A1, a fully Eurasian virus, in commercial poultry in April 2022. All other genotypes identified were reassortants of A1 with North American avian influenza gene segments (denoted with “B”). Genotype B3.3 was a rare genotype prior to the initial spillover into the live bird market system, but remained predominant among backyard flocks in Pennsylvania and surrounding states until September 2023. Genotype B3.3 has not been detected in migratory waterfowl since, suggesting the genotype has waned and is no longer in circulation. This study sheds light on the genotype diversity of H5N1 during the 2022 outbreak in Pennsylvania poultry, contributing to the understanding of virus evolution and its potential impacts. Full article

Tamarindus indica L. is a species of tree with high economic value. However, research on its associated bacterial communities is limited, and no microbial fertilizer has yet been developed specifically for tamarind. In this study, we selected 20 geographical provenances of tamarind as experimental materials, evaluated their germplasm resources, and investigated the correlation between plant traits and associated bacterial communities under grafting conditions. Provenances YM2 and BS21 produced the largest fruits, while all physiological indices showed significant variability among the tested accessions. Microbial samples from the phyllosphere and rhizosphere were collected from these 20 provenances, and 16S rRNA gene sequencing was conducted to compare microbial communities. The differences in rhizosphere microbiota among different samples were more significant than those in phyllosphere microbiota; subsequently, an in-depth investigation was conducted on the relationships between rhizosphere bacterial communities and various traits under these grafting conditions. Through correlation analysis, significant correlations were identified between some microbial phyla and the traits of tamarind under these grafting conditions. Under the current grafting conditions, variations in the rhizosphere microbiome were associated with tamarind provenances. However, due to the constraints of the experimental design, the potential influences of rootstock genotypes and scion–rootstock signal transduction could not be excluded. Nevertheless, through the unification of rootstock sources and the design of correlation analysis, this study has initially verified the dominant association between scion provenances and microbial communities. Full article

Background/Objectives: Late-onset Alzheimer’s disease (LOAD) is a multifactorial neurodegenerative disorder involving the interaction of genetic and environmental factors. Dysregulation of the fibrinolytic system, particularly an increase in plasminogen activator inhibitor-1 (PAI-1) levels, may contribute to Alzheimer’s pathology. Vitronectin (VTN) regulates fibrinolysis by stabilizing PAI-1. This study investigated the relationships between plasma PAI-1 activity and VTN, SERPINE1 (PAI-1), and APOE gene variants in nineteen LOAD patients (>65 years) and ten cognitively normal age-matched control groups. Methods: Targeted next-generation sequencing was used to analyze the VTN, APOE, and SERPINE1 genes in 19 LOAD patients and ten controls. Additionally, plasma PAI-1 activity was measured in both groups. Results: Plasma PAI-1 activity was statistically significantly higher in LOAD patients compared to controls (p = 0.04). Targeted next-generation sequencing results showed that VTN 5′-UTR variants (rs7212814, rs1555584131, rs71135830, and rs11437594) were found in all patients and observed in 20% of controls (p = 0.0001). The VTN rs704 variant was detected in 84% of patients and 29% of controls (p = 0.001). VTN 5′-UTR variants showed Spearman correlation with PAI-1 activity (r = 1.0; p < 0.0001). SERPINE1 3′-UTR variants (rs11178, rs41423845) were found to be associated with the disease (p = 0.027; p = 0.0001). The APOE ε3/ε4 genotype was present in 52.6% of patients and was not associated with PAI-1 activity. VTN variants showed an association with LOAD. Conclusions: These findings suggest that VTN variants may contribute to LOAD pathogenesis by affecting PAI-1 and leading to fibrinolytic system dysregulation. Full article

Hepatitis B virus (HBV) is the smallest partially double-stranded, reverse-transcribing DNA virus, with four open reading frames (ORFs) encoding viral proteins. It is classified into nine geographically distributed genotypes (A–I). In Kenya, the molecular characterization of HBV among patients seeking medical care remains poorly defined. This observational study aimed to characterize HBV among patients seeking medical care in Kenya’s endemic region, focusing on circulating genotypes and ORF mutations. Serum samples were collected from the outpatient departments of selected health facilities, with demographic and clinical information extracted from patients’ medical records. Hepatitis B surface antigen (HBsAg) was tested at the facilities, and 85 HBsAg-positive samples were collected for molecular analysis. The basal core promoter and pre-core (BCP/PC), polymerase, and surface regions of the viral genome were amplified and sequenced to determine genotypes and to profile their mutations. Out of 85 HBsAg-positive samples, 38 samples tested positive for HBV DNA, and 26 samples were successfully sequenced. HBV genotype A was prevalent at 73.1% (19/26), followed by genotype D at 23.1% (6/26), and genotype E at 3.8% (1/26). Genotype A sequences clustered with both A1 Asian and African subgenotypes, whereas genotype D clustered with subgenotypes D6 and D1. All HBV genotype A, D, and E sequences were serotypes adw2, ayw2, and ayw4, respectively. HBV core promoter mutations (A1762T/G1764A) were detected in both genotype D and genotype A isolates. The pre-core G1896A mutation was highly prevalent in genotype D samples (5/6; 83.3%) but was not observed in genotypes A or E. Analysis of mutations within the “a” determinant region revealed genotype-specific patterns: genotype A predominantly harbored V14A, P46H, S58C, and P67Q substitutions; genotype E showed N59S; and genotype D exhibited V14A, C69stop, S104T, and W182stop mutations. Two drug resistance mutations (V191I and A194T) were present in two chronic patients, one with genotype A and the other with genotype D. In conclusion, HBV genotypes A and D are the most prevalent among Kenyan patients with chronic HBV infection. The presence of point mutations in the ORFs among patients seeking medical care highlights the need for molecular surveillance to better understand the viral diversity and its potential clinical and public health implications. Full article

Background/Objectives: Eleocharis ussuriensis Zinserl. is a perennial riparian sedge widely distributed in Northeast Asia and a dominant component of freshwater vegetation in South Korea. However, the intraspecific genetic structure of this species across contrasting hydrological habitats remains insufficiently understood. This study aimed to develop novel SSR markers from whole-genome data and investigate genetic variation and population structure among E. ussuriensis populations in South Korea. Methods: Twenty-one novel simple sequence repeat (SSR) markers were developed from whole-genome sequence data and applied to analyze genetic variation in 120 individuals from 6 populations. Genetic diversity, differentiation, and gene flow were estimated using allele-frequency-based metrics, and population genetic structure was further evaluated using spatial information derived from geographic coordinates. Results: A total of 201 alleles were detected, with a mean polymorphism information content (PIC) of 0.759, indicating high marker informativeness. Mean genetic diversity across populations showed observed heterozygosity (Ho = 0.360) and expected heterozygosity (He = 0.281), while multilocus genotype ratios (G/N) ranged from 0.30 to 1.00 among populations. Genetic differentiation was substantial (F_ST = 0.373–0.669; Jost’s D = 0.540–0.997). Mantel tests revealed that genetic differentiation was significantly correlated with geographic distance (r = 0.67, p < 0.001). Both allele-frequency-based and spatially explicit approaches suggested genetic structuring among populations. Conclusions: The results suggest spatial tendencies in genetic structure among populations, reflecting patterns of allele distribution across regions. These findings provide baseline information on genetic variation in E. ussuriensis and may contribute to a better understanding of its ecological dynamics. Full article

Background/Objectives: Staphylococcus aureus, particularly methicillin-resistant strains, is a leading cause of severe pneumonia. Understanding local molecular epidemiology, including virulence gene profiles and antimicrobial resistance (AMR) mechanisms, is crucial for effective infection control. This pilot study aimed to characterize S. aureus isolates from pneumonia patients in Karaganda, Kazakhstan. Methods: We collected 48 respiratory samples from patients with pneumonia across three medical institutions. Bacterial identification was performed using MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was carried out using European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Whole-genome sequencing of S. aureus isolates was conducted on an Ion Torrent S5 platform. Genomic analysis included multilocus sequence typing (MLST), identification of virulence and AMR genes, and phylogenetic reconstruction. Results: S. aureus was identified in 14.6% (n = 7) of pneumonia cases included in this study. All isolates (100%, n = 7) were phenotypically resistant to benzylpenicillin. The mecA gene was detected in 57.1% of isolates (n = 4), while phenotypic resistance to methicillin was observed in 28.6% (n = 2) of the isolates. Resistance to azithromycin (57.1%, n = 4) and levofloxacin (42.9%, n = 3) was observed among the isolates. Two isolates (28.6%) were multidrug-resistant (MDR). Genomic analysis revealed the prevalence of the ST22 clone (57.1%, n = 4) in the studied cohort. Other sequence types were ST97, ST8, and ST45 (14.3% each). Phylogenetic analysis showed clustering consistent with MLST profiles. All isolates carried a conserved core virulence arsenal, including hemolysin (hla, hlg), biofilm-forming genes (icaADBC), immune evasion genes (sak, scn), and iron acquisition genes (isd). The Panton–Valentine leukocidin (PVL) genes were detected in three isolates. AMR gene analysis revealed the ubiquitous presence of mepA and tetracycline efflux pump genes, along with regulatory genes (arlRS, mepR, mgrA). The blaZ and ermA genes were not detected despite high phenotypic resistance to penicillin and macrolides. Conclusions: This study reports the identification of the virulent and resistant ST22 S. aureus clone in pneumonia cases in Karaganda, Kazakhstan. The discordance between phenotypic and genotypic AMR profiles underscores the necessity for integrated diagnostic approaches. Full article

Staphylococcus aureus is a high-priority pathogen causing skin and soft tissue infections (SSTIs). The frequent resistance to anti-staphylococcal agents exhibited by this underscores the need for accurate diagnostics to guide effective therapy. Therefore, this study aimed to compare phenotypic and genotypic resistance in S. aureus isolates from nasal carriers and SSTIs and to elucidate gene-silencing mechanisms. In total, 355 S. aureus isolates (256 isolated from carriers and 79 from SSTIs) were studied for their phenotypic and genotypic resistance to β-lactams, macrolides, tetracyclines, aminoglycosides, and mupirocin. The silenced mupA gene (low prevalence: 0.6%; 2/335), linked to mupirocin resistance, was sequenced, and expression was assessed via reverse transcription qualitative PCR (RT-qPCR) in all mupA-positive isolates. SSTI isolates showed significantly higher resistance to erythromycin, gentamicin, and mupirocin, along with a higher prevalence of multidrug-resistant strains and ermC and tetM genes. Sequencing revealed multiple mutations in silent mupA, including a critical frameshift (c.372 delA) in a poly(A) tract that brings about premature truncation. RT-qPCR indicated upregulation of silent mupA variants and high variability in functional strains, suggesting that frameshift alone prevents resistance. These findings highlight silent resistance genes as key targets for advancing S. aureus surveillance and for combating emerging threats. Full article

Cystic echinococcosis (CE) is caused by a tapeworm of the Echinococcus granulosus s.l. species complex belonging to the Taeniidae family. CE affects more than 100 countries, including Poland, while remaining a significant public health threat to both humans and livestock. The aim of this study was to identify the genotypes responsible for cases of cystic echinococcosis in Poland by conducting molecular analysis of larvae isolated from Polish patients, and to investigate the diagnostic pathways leading to CE diagnosis. Between April 2023 and January 2025, tissue samples were collected from 10 patients following hepatectomy. Analysis of diagnostic pathways revealed that radiological findings followed by PCR or histopathological testing were sufficient to establish a reliable diagnosis of CE in 90% and 100% of cases, respectively. Serological tests showed lower sensitivity, reaching 86% for ELISA and 71% for Western blot. DNA extracted from all samples was used as the template in PCR to amplify and sequence the region of the mitochondrial NADH dehydrogenase 1 gene (nad1). PCR analysis confirmed presence of Echinococcus granulosus s.l. species in eight cases. All obtained nad1 sequences showed identity with the Echinococcus canadensis G7 (pig) strain. These results indicate that it remains the most frequent causative agent of human cystic echinococcosis in Poland. Full article

Genotyping is a key step in molecular breeding. Due to its cost-effectiveness, accuracy, and flexibility, genotyping by target sequencing (GBTS) has become a preferred technology for medium-density genotyping. In this study, a new GBTS array for fresh edible maize was developed using resequencing data from 477 lines. The array contains 5759 SNPs evenly distributed across the maize genome, with average minor allele frequency (MAF) and polymorphism information content (PIC) values of 0.40 and 0.36, respectively. These SNPs are closely associated with 1566 functional genes. Cluster analysis of 198 maize lines based on the GBTS array was consistent with their pedigree relationships. Furthermore, 277 fresh waxy maize lines were genotyped and used for genomic selection analyses of hundred-kernel weight, kernel length, and kernel width. Comparative evaluation of different models indicated that Ridge Regression Best Linear Unbiased Prediction (rrBLUP) was the optimal model, with prediction accuracies of 0.33, 0.64, and 0.36, respectively. Additional analyses using different marker densities based on the rrBLUP model showed that prediction accuracy did not increase when the number of markers exceeded 2000, indicating that this array provides sufficient marker density for genetic analysis and genomic selection. Overall, this array provides a useful tool for genetic studies of fresh edible maize and facilitates the application of genomic selection in breeding programs. Full article

Avian reovirus (ARV) causes viral arthritis and leads to considerable economic losses in the poultry industry. In this study, six ARV strains of distinct genotypes (FJNP01–FJNP06) were isolated from commercial broiler farms. Through gene sequencing and pathogenicity assessment, we analyzed the genetic evolution and pathogenic characteristics of the σC, P10, σB, μB, and λC genes. Pathogenicity tests revealed that inoculation with FJNP01–FJNP06 by footpad or oral gavage induced symptoms in specific-pathogen-free (SPF) chickens, including mortality and growth retardation. Among the isolates, FJNP04 (genotype IV) showed the highest pathogenicity, causing increased mortality, weight loss, and severe lesions in the footpads and bursa of Fabricius, followed by FJNP05 and FJNP02. The pathogenicity of FJNP06 varied by inoculation route, with enhanced pathogenicity observed following oral gavage. In contrast, FJNP01 and FJNP03 demonstrated relatively low pathogenicity. Identity analysis indicated that σC and P10 were highly variable, σB was relatively conserved, while μB and λC displayed considerable divergence. Phylogenetic analysis placed FJNP01–FJNP06 into genotypes I to VI, respectively, forming six distinct branches on the σC and P10 phylogenetic trees, yet clustering more closely on the σB, μB, and λC trees. The pathogenicity of different genotypes of ARV varies, among which FJNP04 (genotype IV) exhibits the strongest pathogenicity. Genetic sequence analysis revealed that σC and P10 are highly variable, σB is relatively conserved, while μB and λC display a wide range of variation. This study provides insights into the genetic variation and pathogenic characteristics of ARV and serves as a reference for future research. Full article

Chinese cabbage is one of the major vegetable crops in northern Asia. Its leaves are the major organ for photosynthesis and production, and leaf color directly influences its yield and quality. Here, we obtained a pale green mutant pgm3. This mutant line was derived from EMS mutagenesis of Chinese cabbage DH line FT. pgm3 exhibited chlorosis and etiolation, delayed growth, reduced photosynthetic pigment content and net photosynthetic rates, and impaired development of the chloroplast inner membrane system. Genetic analysis revealed that the pale green phenotype was controlled by a single recessive nuclear gene, Brpgm3. Mutmap analysis indicated that Brpgm3 is located on a 13.9 Mb region in A03. Within this region, a single SNP (A03: 7194530) with an SNP-index of 1, located in BraA03g015750.3C (BrClpC1), was identified from 40 differential SNPs. KASP genotyping demonstrated that the SNP co-segregated with the pale green phenotype in the F₂ population. Sanger sequencing confirmed a G-to-A SNP in exon 4 of BrClpC1, which resulted in an amino acid substitution from S to G. Furthermore, multiple sequence alignment of homologs from 28 species demonstrated that this mutated residue is highly conserved. BrClpC1 was predominantly expressed in leaves and exhibited the highest transcript abundance among the nine members of the Class I Clp gene family in Brassica rapa. This is the first report identifying ClpC1 in Brassica crops. Our results not only confirmed BrClpC1 as a strong candidate gene for the pale green mutant of Chinese cabbage, but also highlighted BrClpC1 as a target for chloroplast biology research in Brassica crops. Full article

Bovine rotavirus (BRV) poses a major threat to the global cattle industry, driving significant morbidity and mortality in young calves. In Yunnan Province, China, BRV is the primary cause of neonatal calf diarrhea (NCD), yet the molecular epidemiology of circulating strains remains poorly understood. This study aimed to investigate the molecular characteristics of bovine rotavirus strains associated with a severe outbreak of the NCD on a local farm. Fecal samples were collected from 396 calves and screened for BRV by RT-PCR targeting the VP6 gene. Positive samples were subjected to virus isolation in MA104 cells, followed by whole-genome sequencing, phylogenetic analysis, and pathogenicity assessment in suckling mice. Of 396 samples, 85 tested positive for BRV, corresponding to an animal-level prevalence of 21.5% (95% CI: 17.5–25.8%), with four fatalities recorded. A strain designated as BRV-YN1-2021 was successfully isolated, exhibiting characteristic cytopathic effects, specific immunofluorescence, and typical rotavirus morphology by electron microscopy. Genomic analysis revealed the constellation G8-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, identified as genotype G8P[1]. BLAST analysis showed that four genomic segments shared the highest identity with deer rotavirus strains, five with human rotavirus strains, and two with bovine rotavirus strains. Phylogenetic analysis demonstrated close relationships with US deer strains, Japanese bovine strains, and human strains circulating in China. Experimental infection in suckling mice induced diarrhea and significant intestinal histopathology, degeneration of villous epithelial cells, goblet cell hyperplasia, and inflammatory infiltration. This study reports the first isolation of a G8P[1] bovine rotavirus from a diarrhea outbreak in Chinese cattle. The multi-host genetic composition provides evidence of interspecies reassortment events, highlighting the zoonotic potential of BRV and emphasizing the need for continuous molecular surveillance to inform effective control strategies. Full article

Background/Objectives: The Korean Global Antimicrobial Resistance Surveillance System monitors bloodstream Staphylococcus aureus infections by combining antimicrobial susceptibility testing (AST) with conventional polymerase chain reaction (PCR). Considering the clinical significance of methicillin-resistant S. aureus (MRSA), we performed an in-depth analysis of isolates showing genotypic–phenotypic discrepancies. Methods: Isolates were collected from designated collection centers in the Republic of Korea between 2017 and 2024. The 30 μg cefoxitin disk diffusion method was used to define the phenotypes. PCR targeting mecA and the staphylococcal cassette chromosome mec (SCCmec) was used to identify genotypes through gel electrophoresis. Long-read whole-genome sequencing (WGS) was performed using the Revio system (Pacific Biosciences) for isolates exhibiting discrepancies between phenotypes and genotypes. Results: In total, 5808 isolates were screened, and seven cases of genotypic–phenotypic discrepancies were identified, including one infant and six elderly patients with chromosomal SCCmec type IV. Although WGS confirmed intact PCR primer-binding sites, structural alterations were observed: three isolates had normal-length mecA and mecR1, two had partial deletions in mecA, and two featured either mecA or mecR1 split into two proteins. Notably, although the six isolates with intact mecR1 genes matched the nucleotide length of SCCmec type IV, their sequences exhibited high homology with SCCmec type II. Conclusions: Despite the presence of mecA, the non-standard configuration of regulatory genes within the SCCmec elements suppressed actual resistance expression. Because conventional PCR focusing on partial gene segments could overlook such phenotypic traits, the meticulous observation and implementation of WGS are crucial for the accurate characterization of genotypic–phenotypic discrepancies. Full article