Search Results (2,644)

Emericellopsis species from extreme environmental conditions provide a rich source of unique and biologically active secondary metabolites. The paper exhibits a comprehensive genomic analysis including complete genome sequencing, phylogenetic reconstruction, and functional annotation of two Emericellopsis species from highly saline and alkaline coastal soil ecosystems. Comparative genomics has been applied to reveal the genetic evolution, metabolic diversity, and environmental adaptation of the Emericellopsis genus. The genomes of E. alkalina E101 and E. fimetaria p24 have been found to encode various enzymes, including carbohydrate-active enzymes such as endoxylanases, that are useful for many ecological adaptations. The genomes of E. alkalina E101 and E. fimetaria p24 feature numerous biosynthetic gene clusters (BGCs), capable of synthesizing both known and potentially novel secondary metabolites with antimicrobial activity. Some BGCs show similarity to those producing known secondary metabolites, such as leucostatin A/B, clavaric acid, ascochlorin, (-)-mellein, and apicidin, among others. However, the majority of BGCs do not display any known similarities. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of Emericellopsis fungi and may serve as a highly useful tool within biotechnological applications. Full article

Brown spot on the leaf sheath is an emerging disease of sweet corn (Zea mays L.) in Sinaloa, Mexico, with an unknown etiology. This study aimed to identify the causal agent of the disease and assess its pathogenicity on commercial sweet corn hybrids. Bacterial strains were isolated from symptomatic leaf sheaths collected from commercial fields. Identification was performed through biochemical profiling (API 50CHB/E), pathogenicity tests on alternative hosts (potato, onion, celery), and molecular analysis (16S rRNA and recA genes sequencing and phylogenetic reconstruction). Pathogenicity and virulence were confirmed by inoculating four sweet corn hybrids in a greenhouse. The strains were Gram-negative rods, identified as Burkholderia gladioli based on biochemical profiles and molecular data (99% 16S rRNA+ recA similarity; phylogenetic clustering within the B. gladioli clade). In greenhouse trials, the strains induced brown spot lesions on the leaf sheaths of all tested hybrids, replicating field symptoms fulfilling Koch’s postulates. This is the first report of B. gladioli as the causal agent of brown spot on the leaf sheath of sweet corn in Mexico. The pathogen’s broad host range highlights its potential as an emerging threat to horticultural crops in the region. Full article

The Eurasian lynx (Lynx lynx) is an apex predator and an important sentinel for trophically transmitted helminths acquired via predation on wild ungulates. On 2 March 2022, an adult male lynx that was road-killed in the Apuseni Mountains (Surducel hunting ground, Bihor County) was collected, frozen for biosafety, and a necropsy was performed. Taeniid cestodes were detected, with a total intestinal burden of nine adult specimens. Genetic analyses confirmed Taenia lynciscapreoli, and the obtained sequences were deposited in GenBank (PV843597, PV855065, PV844409). Phylogenetic inference based on cox1 assigned the Romanian isolate within the European cluster, distinct from the Chinese isolate, while showing genetic proximity to Taenia sp. (MW846305) that have been reported from a lynx in China. This study represents the first molecular identification of T. lynciscapreoli in the Eurasian lynx in Romania and, to our knowledge, the first record from Southeastern Europe. 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

Human parainfluenza virus type 4 (hPIV4) remains poorly characterized compared with other hPIV serotypes and information on its genomic diversity is particularly limited for Russia and Eastern Europe. In this study, we report the first complete genome sequences of hPIV4 isolates from Russia and place them in the context of global hPIV4 genetic diversity. Eight hPIV4 viruses were isolated in cell culture from respiratory samples collected from hospitalized children in Saint Petersburg between 2017/2018 and 2023/2024. Complete viral genomes were recovered using a metagenomic whole-genome amplification approach based on SMART-9N technology. Phylogenetic analysis of 178 complete hPIV4 genomes showed clear separation into hPIV4a (n = 132) and hPIV4b (n = 46) subtypes. Based on genetic distance approach, hPIV4a formed two major clusters, with the dominant cluster B subdivided into four subclusters (B1–B4); and subcluster B4 further resolved into four genetic lineages. All Russian isolates belonged to the subcluster B4 and were distributed among multiple co-circulating lineages. In contrast, hPIV4b genomes segregated into three distinct clusters, reflecting structured genetic diversity within the subtype. Collectively, this study provides, to the best of our knowledge, the first p-distance-based framework for hPIV4 whole-genome classification and contributes new complete genome sequences for an underrepresented region. Full article

Grain number and size are important agronomic traits determining grain yield, and yield improvement depends on exploring functional variations of key regulatory genes. Mitogen-activated protein kinase 6 (MAPK6) plays a key role in crop development; however, its function and variation in wheat remain largely unclear. In this study, we aimed to characterize the function and haplotype variations of TaMAPK6-7A in wheat and develop functional molecular markers for marker assisted breeding. We identified three TaMAPK6 homoeologs on 7A, 7B, and 7D in wheat through bioinformatics analysis and revealed their evolutionary trajectory by phylogenetic analysis, with clear monocot-dicot lineage divergence and TaMAPK6 homoeolog clustering matching with hexaploid wheat’s allopolyploid origin. Spatiotemporal expression analysis showed that the TaMAPK6 homoeologs constitutively expressed in wheat tissues and were highly abundant in endosperm, spike, grain, and anther, with TaMAPK6-7A showing slightly higher transcript levels. In an ethyl methanesulfonate (EMS)-induced Jing411 mutant library, we identified a loss-of-function mutant of TaMAPK6-7A (J7633452), which exhibited severely reduced grain number per spike, impaired anther fertility, and increased grain size. Natural variation analysis of a large set of wheat accessions identified two major haplotypes of TaMAPK6-7A, with Type I was identical to the reference genome cultivar ‘Chinese Spring’, and Type II was consistent with the elite wheat cultivar ‘AK58’. We developed a PCR marker to accurately distinguish the two haplotypes and genotyped 192 wheat cultivars and elite breeding lines. Phenotypic evaluation indicated that Type II was an elite haplotype significantly associated with higher grain number per spike. This study characterizes TaMAPK6-7A as a key regulator of grain number per spike, providing a gene and molecular marker for marker-assisted breeding to improve grain yield. Full article

The first influenza A(H5N1) human case associated with the A(H5N1) dairy cattle outbreak in the United States was identified in April 2024. The U.S. CDC response to this outbreak was activated days later and remained active until July 2025. During this time, 70 human cases of influenza A(H5N1) were detected with a range of epidemiological links to sources of exposure. Next-generation sequencing (NGS) of human samples was an effectual mechanism for tracking and analyzing the outbreak evolution throughout the response. Due to the specimens’ importance and their variable physical quality, an assortment of laboratory methods was utilized including influenza segment-specific amplification, enrichment capture, short-read, and long-read sequencing. Combining these methods allowed for high-quality genomic data production with rapid turnaround times—typically 2 days from sample receipt to public database submission. By leveraging replicate sequencing, enrichment capture, and sequencing of diagnostic amplicons, valuable genomic data could be produced directly from human clinical specimens that would have normally been considered too weak for routine virologic surveillance sequencing. The resulting assemblies were characterized and analyzed by CDC and shared with local and state public health authorities to facilitate case investigations and risk assessment. These data were further used for phylogenetic analyses of viruses from human cases to investigate likely animal-to-human transmission events and identify clusters within the outbreak that might indicate trends in the types of exposures. Through the adaptable laboratory workflow and the rapid release of viral genomic data, the public health risk mitigation strategies could be evaluated and adjusted in real time. 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

Haptophytes are ubiquitous single-celled eukaryotic plankton in coastal and open oceans that play a key role in marine biogeochemical cycling. Understanding the size structure and community composition of active haptophytes is crucial for elucidating their diversity and ecological functions. This study investigated the diversity and community structure of pico- (0.2–3 μm) and nano-sized (3–20 μm) haptophytes in the surface waters of the western Pacific Ocean using high-throughput sequencing targeting the hypervariable V4 region of the 18S rRNA. The pico-sized community exhibited significantly higher diversity than the nano-sized community. Community composition varied significantly between size fractions, driven primarily by the genera Chrysochromulina and Syracosphaera. Furthermore, the nano-sized community was more strongly influenced by environmental variables than the pico-sized community, although neither size fraction displayed a clear coastal-to-open-ocean distribution pattern. Null and neutral community model analyses indicated that both size-fractionated communities were primarily regulated by stochastic processes, while deterministic processes exerted a greater influence on the nano-sized community. Co-occurrence network analysis revealed stronger interconnections and a higher number of keystone species within the nano-sized community. In both networks, intermediate taxa (relative abundances of 0.01% to 0.1%) exhibited the highest diversity and abundance among keystone species, highlighting their pivotal role in shaping the network structure and stability. Additionally, phylogenetic analyses revealed that while the majority of ZOTUs clustered with known taxa, multiple deep-branching, uncultured lineages were identified across both size fractions, indicating substantial uncharacterized genetic diversity. This study underscores the variability and hidden diversity of size-fractionated haptophyte community structures in oligotrophic open oceans, providing valuable insights into their functional significance in global biogeochemical cycles. Full article

The objectives of this paper were to assess the genetic diversity, population structure, genetic differentiation, and phylogenetic relationships among seven duck populations using 14 microsatellite (MS) markers. This paper included 176 individuals representing seven duck populations of Bangladesh: indigenous duck (BLD), Nageswari (NAG), Rupali (RUP), Jinding (JIN), Pekin (PEK), BAU Black and White (BWC), and BAU White (WHC). A total of 133 alleles were observed with a mean of 9.50 alleles per locus. Genetic diversity was evaluated using measures such as allele frequency, observed and expected heterozygosity, and Shannon’s information index with average values of 5.44 ± 0.31, 0.59 ± 0.02, 0.64 ± 0.02, and 1.28 ± 0.05, respectively. Population differentiation and inbreeding analysis (F-statistics) indicated moderate genetic diversity and a slight degree of inbreeding across populations. Analysis of molecular variance indicated that 75% of the total genetic diversity was attributable to the within-population variation, whereas 9% and 16% were attributed to the variation among individuals and population differentiation, respectively. Indigenous duck populations (BLD, NAG, and RUP) had a close genetic relationship with JIN ducks and an intermediate relationship with two crossbreds (BWC and WHC), and the highest genetic distance was observed with PEK ducks. Neighbor-joining phylogenetic analysis revealed that the Bangladeshi indigenous duck populations formed a single cluster, while the two crossbreds (BWC and WHC) and PEK exhibited their distinct genetic identities in separate clusters. Furthermore, structure analysis at K = 2 to 5 confirmed the distinct genetic architecture (ΔK = 4.00) of the studied duck populations. This paper provides important insights into genetic diversity measures and population differentiation that will be helpful in future genetic improvement, conservation initiatives, and the design of appropriate breeding programs. Full article

Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic research. Taxonomists have alternately split and combined morphotypes of Pediomelum tenuiflorum for two centuries. With samples of P. tenuiflorum from across its distribution, this research aimed to (1) infer a robust phylogeny using molecular data, i.e., gene sequences from chloroplast and nuclear genomes; (2) assess genetic diversity using molecular markers, specifically Inter Simple Sequence Repeats (ISSRs); (3) provide evidence to support the taxonomic placement and possible splitting of P. tenuiflorum; and (4) identify consistent morphological characteristics using a correlation matrix to distinguish among the morphotypes. Results: Striking morphological differences among the individuals of P. tenuiflorum from across the species’ distribution resulted in more than two morphotypes. Phylogenetic data suggest hybridization is occurring among genetically and morphologically distinct members of P. tenuiflorum and with other species in the genus Pediomelum, whereas ISSR results indicate detectable genetic variation but do not resolve discrete clusters. This study reports the first ISSR markers used to assess genetic diversity in Pediomelum species. Conclusions: Morphological and genetic variation exist across individuals of P. tenuiflorum but not in monophyletic groups that support splitting the morphotypes into multiple species. Future investigations into chromosome numbers might reveal polyploidization in the lineage, and phylogenies estimated from low-copy nuclear genes could elucidate hybridization pathways. Full article

Rabies is a fatal zoonotic disease once clinical symptoms develop. In Europe, sustained animal rabies control programs have led to a marked decline in animal rabies and subsequently human rabies cases; however, sporadic infections continue to occur. In July 2025, a fatal case of autochthonous (locally acquired) human rabies was confirmed in Romania following a stray dog bite in a patient who did not receive post-exposure prophylaxis (PEP). Here, we report the first molecular characterization of a human rabies virus (RABV) strain isolated in Romania and place it in the context of contemporaneously circulating animal-derived RABV strains. Rabies virus infection was confirmed intra vitam by fluorescent antibody testing and both conventional and real-time RT-PCR on cerebrospinal fluid and saliva, with postmortem confirmation on skin and brain tissue. Whole-genome sequencing was performed on the human isolate and on 22 animal-derived RABV strains collected in northern Romania in 2025. Phylogenetic analyses revealed that all recent Romanian sequences clustered within the North-East European (NEE) rabies virus phylogenetic group and segregated into two geographically distinct genetic clusters: a north-western cluster, closely related to strains from Slovakia and Poland, and a larger north-eastern cluster, linked to viruses circulating in eastern Romania and the Republic of Moldova. The human-derived RABV genome was grouped within the north-eastern cluster and showed the highest genetic similarity to animal viral strains from the same geographical area, supporting a local transmission event. This demonstrates the importance of integrating human viral genomic data into the national rabies surveillance framework. Full article

Pigeonpox is a significant infectious disease caused by Pigeonpox virus (PPV), which severely impacts the pigeon industry. Current control methods primarily rely on heterologous vaccines, such as those derived from avian poxviruses, but their protection is limited, creating an urgent need for the development of a specific vaccine. In this study, 720 samples collected from several regions of China between 2022 and 2023 were tested for PPV, followed by virus isolation, identification, and genetic evolutionary analysis. Based on these findings, complete genome sequencing and attenuation of the representative BJ-02 isolate were conducted, and the potential of this strain as a candidate for an attenuated vaccine was preliminarily evaluated. The survey showed PCR positive rates of 9.05%, 16.11%, and 12.50% in samples from Beijing, Guangdong, and Hainan, respectively. Six viral strains were isolated, all of which produced typical lesions on chorioallantoic membranes (CAM) and chicken embryo fibroblasts (CEF). Phylogenetic analysis based on the P4b gene revealed that the six viruses clustered within the same evolutionary branch, closely related to PPV and penguinpox virus strains from South Africa, India, and Taiwan, China. Complete genome sequencing of the BJ-02 strain showed its genomic structure to be similar to that of other fowlpox viruses, with some differences. After serial passage in CAM, PEF and CEF, the BJ-02 SD55 high-passage strain adapted well to in vitro culture, exhibited significantly reduced pathogenicity in chicken embryos and pigeons, and showed no reversion to virulence after five consecutive back-passages. Animal immunization tests demonstrated that the BJ-02 SD55 suspected attenuated strain induced specific antibodies and provided 100% protection against challenge with the virulent strain. In conclusion, PPV is widely prevalent in China. The BJ-02 strain, successfully isolated and attenuated through serial passage, demonstrates excellent immunogenicity and high safety, making it a promising candidate for a specific pigeonpox vaccine. Additionally, the complete genome characterization of BJ-02 contributes to the avian poxvirus genome database and provides critical data to support research on viral pathogenesis and the development of viral vector vaccines for avian and potentially mammalian species. Full article

Background: Fruit texture is a major component of plum quality, affecting both consumer acceptance and postharvest behavior. Pectin methylesterases (PMEs) play important roles in cell-wall pectin modification and are therefore likely to contribute to plum fruit texture development and ripening-associated softening. However, the PME gene family has not yet been comprehensively investigated in plum (Prunus salicina L.). Methods: In the present study, a chromosome-level plum genome was used to survey this gene family at the whole-genome scale. Phylogenetic relationships, chromosomal positions, exon–intron organization, conserved motifs, domain architectures, gene duplication, and cis-elements were analyzed. Four flesh texture traits were measured in 55 plum accessions to characterize texture variation and select two representative cultivars with contrasting flesh textures for further molecular analysis. Based on the clustering results, ‘WSCL’ and ‘FR’ were selected for expression profiling during fruit development and subsequent correlation analysis with texture traits. Results: A total of 46 PsPME genes were identified. Phylogenetic analysis classified them into four major subgroups. Structural analyses indicated an overall conserved family framework, although noticeable variation was retained among individual members. Dispersed duplication made the largest contribution to family expansion, and most duplicated pairs appeared to have evolved under purifying selection. Correlation analysis showed that PsPME20, PsPME22, and PsPME25 were significantly negatively correlated with flesh firmness, while PsPME20 was additionally linked to flesh compactness and flesh fragility. Conclusions: Overall, this study clarifies the structural and evolutionary characteristics of the PsPME family and identifies candidate genes that may contribute to texture differences in plum, offering a basis for future functional studies and breeding programs. Full article

Hepatitis E virus (HEV) is a zoonotic pathogen of global concern that circulates in both domestic and wild swine populations. Understanding its presence and dynamics in wildlife reservoirs is crucial for assessing spillover risks and designing One Health surveillance strategies. This study investigated the occurrence, genetic diversity, and evolutionary relationships of HEV in wild boars from mainland Portugal. A total of 120 animals from seven districts were tested, with HEV RNA detected in four cases (3.3%), all from the Évora district near the Spanish border. One positive sample was successfully sequenced, and phylogenetic analysis based on the complete genome classified it within the HEV-3m subtype, clustering with predominantly human-derived sequences from Spain and France, which highlights its zoonotic potential. A second phylogenetic analysis based on a partial genomic fragment, including sequences from domestic pigs in Portugal, revealed the co-circulation of subtypes 3e, 3f, and 3m without clear spatial or temporal patterns. Phylogeographic analysis suggested that the identified strain was most likely introduced from Spain, supporting the hypothesis of cross-border transmission through wild boar movement. No recombination events were detected in the sequence obtained in this study. These findings provide the first molecular evidence of HEV-3m circulation in wild boars in Portugal, offering valuable insight into the HEV strain circulation in European wildlife populations. The zoonotic potential of HEV and the likelihood of interspecies transmission highlight the need for coordinated cross-border surveillance and integrated One Health strategies. Full article