Search Results (2,245)

Papillomaviruses (PVs) are double-stranded DNA viruses known to induce a variety of epithelial lesions in dogs, ranging from benign hyperplasia to malignancies. In regions of rich biodiversity such as the Western Amazon, data on the circulation and genetic composition of canine papillomaviruses (CPVs) remain scarce. This study investigated CPV types present in oral and cutaneous papillomatous lesions in domiciled dogs from Acre and Rondônia States, Brazil. Sixty-one dogs with macroscopically consistent lesions were clinically evaluated, and tissue samples were collected for histopathological examination and PCR targeting the L1 gene. Among these, 37% were histologically diagnosed as squamous papillomas or fibropapillomas, and 49.2% (30/61) tested positive for papillomavirus DNA. Sequencing of the L1 gene revealed that most positive samples belonged to CPV1 (Lambdapapillomavirus 2), while one case was identified as CPV8 (Chipapillomavirus 3). Complete genomes of three CPV1 strains were obtained via high-throughput sequencing and showed high identity with CPV1 strains from other Brazilian regions. Phylogenetic analysis confirmed close genetic relationships among isolates across distinct geographic areas. These findings demonstrate the circulation of genetically conserved CPVs in the Amazon and reinforce the value of molecular and histopathological approaches for the accurate diagnosis and surveillance of viral diseases in domestic dogs, especially in ecologically complex regions. Full article

Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article

The goal of phylogeography is to explain how microevolutionary forces shape the gene pool of a lineage into the geography. In this study we have evaluated the amount of genetic variation in 13 populations of Dorymyrmex bicolor distributed in a mountainous region in Central Veracruz, Mexico. To do so, we sequenced fragments from the mitochondrial COI, COII, and nuclear LWRh genes. Segregated sites were found only at the mitochondrial markers, recovering a total of 21 different haplotypes. The nucleotide diversity ranged from 0 to 0.5% at the different sampling sites. Phylogenetic and spatial analyses of molecular variance revealed a weak but significant phylogeographic structure associated with lowland and mountainous zones. Molecular clock analysis suggests that radiation in the mountain area started 7500 years ago, whereas lineage radiation in the lowland started more recently, around 2700 years ago. The phylogeographic structure is incipient, with nests from lowlands more closely related to mountain nests than to other lowland nests, and vice versa. This seems to be consistent with a model of incomplete lineage sorting. The obtained patterns appear to be the result of restricted gene flow mediated by a complex topographic landscape that has been shaped by a dynamic geologic history. Full article

This study analyzed the heavy metal tolerance and chromium reduction and the potential of plant growth to promote Rhizobium sp. OS-1. By genetic makeup, the Rhizobium strain is nitrogen-fixing and phosphate-solubilizing in metal-contaminated agricultural soil. Among the Rhizobium group, bacterial strain OS-1 showed a significant tolerance to heavy metals, particularly chromium (900 µg/mL), zinc (700 µg/mL), and copper. In the initial investigation, the bacteria strains were morphologically short-rod, Gram-negative, appeared as light pink colonies on media plates, and were biochemically positive for catalase reaction and the ability to ferment glucose, sucrose, and mannitol. Further, bacterial genomic DNA was isolated and amplified with the 16SrRNA gene and sequencing; the obtained 16S rRNA sequence achieved accession no. HE663761.1 from the NCBI GenBank, and it was confirmed that the strain belongs to the Rhizobium genus by phylogenetic analysis. The strain’s performance was best for high hexavalent chromium [Cr(VI)] reduction at 7–8 pH and a temperature of 30 °C, resulting in a total decrease in 96 h. Additionally, the adsorption isotherm Freundlich and Langmuir models fit best for this study, revealing a large biosorption capacity, with Cr(VI) having the highest affinity. Further bacterial chromium reduction was confirmed by an enzymatic test of nitro reductase and chromate reductase activity in bacterial extract. Further, from the metal biosorption study, an Artificial Neural Network (ANN) model was built to assess the metal reduction capability, considering the variables of pH, temperature, incubation duration, and initial metal concentration. The model attained an excellent expected accuracy (R² > 0.90). With these features, this bacterial strain is excellent for bioremediation and use for industrial purposes and agricultural sustainability in metal-contaminated agricultural fields. Full article

Pleurotus ostreatus is a widely cultivated edible fungus in China, renowned for its rich nutritional composition and diverse medicinal compounds. However, the quality of the currently published P. ostreatus genomes remained suboptimal, which limited in-depth research on its evolution, growth, and development. In this study, we conducted a chromosome-level genome assembly of the monokaryotic basidiospore strain PC80. The assembled genome spanned 40.6 Mb and consisted of 15 scaffolds. Ten of these scaffolds contained complete telomere-to-telomere structures. The scaffold N50 value was 3.6 Mb. Genome annotation revealed 634 carbohydrate-active enzyme (CAZyme) family genes. Through collinearity analysis, we further confirmed that the PC80 genome exhibited higher completeness and greater accuracy compared to the currently published genomes of P. ostreatus. At the matA locus of PC80, three hd1 genes and one hd2 gene were identified. At the matB locus, seven pheromone receptor genes and two pheromone precursor genes were detected. Further phylogenetic analysis indicated that three of these pheromone receptor genes are likely to have mating-specific functions. This complete genome assembly could provide a foundation for future genomic and genetic studies, facilitate the identification of key genes related to growth and developmental regulation, and promote technological innovations in P. ostreatus breeding and efficient utilization. Full article

This study describes the characterization of a novel thermostable α-amylase from a Bacillus licheniformis 104.K strain isolated from the Kashkadarya region of Uzbekistan. Phylogenetic analysis revealed that the thermostable α-amylase belongs to glycoside hydrolase family 13 subfamily 5 (GH13_5) and shares high sequence similarity with known α-amylases. Our results demonstrate that the recombinant α-amylase exhibits optimal activity at pH 6.0 and 90 °C, retaining full activity after 30 min at 60 °C. The addition of CaCl₂ significantly enhanced thermostability, with the enzyme retaining more than 95% of its initial activity at 70 °C after 30 min. Our findings indicate that α-amylase from B. licheniformis 104.K is a functional, thermostable enzyme with potential industrial applications. This study highlights the commercial significance of thermostable amylases and the need to identify novel, cost-effective, and sustainable sources. The results of this study will contribute to the fields of enzyme applications, stabilizing additives, and genetic engineering of thermostable genes. Full article

Peanut (Arachis hypogaea L.) is a globally important oilseed cash crop, yet its limited genetic diversity and unique reproductive biology present persistent challenges for conventional crossbreeding. Traditional breeding approaches are often time-consuming and inadequate, mitigating the pace of cultivar development. Essential for double fertilization and programmed cell death (PCD), DUF679 membrane proteins (DMPs) represent a membrane protein family unique to plants. In the present study, a comprehensive analysis of the DMP gene family in peanuts was conducted, which included the identification of 21 family members. Based on phylogenetic analysis, these genes were segregated into five distinct clades (I–V), with AhDMP8A, AhDMP8B, AhDMP9A, and AhDMP9B in clade IV exhibiting high homology with known haploid induction genes. These four candidates also displayed significantly elevated expression in floral tissues compared to other organs, supporting their candidacy for haploid induction in peanuts. Subcellular localization prediction, confirmed through co-localization assays, demonstrated that AhDMPs primarily localize to the plasma membrane, consistent with their proposed roles in the reproductive signaling process. Furthermore, chromosomal mapping and synteny analyses revealed that the expansion of the AhDMP gene family is largely driven by whole-genome duplication (WGD) and segmental duplication events, reflecting the evolutionary dynamics of the tetraploid peanut genome. Collectively, these findings establish a foundational understanding of the AhDMP gene family and highlight promising targets for future applications in haploid induction-based breeding strategies in peanuts. Full article

Scale insects, which belong to the superfamily Coccoidea within the order Hemiptera, encompass more than 8000 species worldwide. The adult females of these species are characterized by their immobility, and often lack wings and legs. Scale insects feed on plant tissues and can cause significant agricultural damage as pests. This study presents the sequencing of five coccoid mitogenomes, revealing detailed annotations and comparisons with other Hemiptera. The sequencing yielded between 73 million and over 121 million reads, allowing for the reconstruction of mitogenomes ranging from 12,821 to 14,446 nucleotides. Notably, a high A + T content was observed across the newly sequenced mitogenomes. Gene rearrangements were identified in all five newly sequenced mitogenomes, with the evolutionary rate analysis indicating that Coccoidea exhibit the highest Ka and Ka/Ks values among the hemipterans. In a phylogenetic context, the mitogenomes of representative species from Coccoidea and Aleyrodoidea exhibit more frequent mitochondrial gene rearrangements than those of other hemipteran groups. The analysis suggests that the frequent mitochondrial gene rearrangements observed in the coccoid species are associated with accelerated nucleotide substitution rates, supporting a connection between genetic evolution and structural variation in mitogenomes. Full article

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

Background/Objectives: Lactiplantibacillus plantarum is widely utilized in the fermentation industry and offers potential health benefits. However, large-scale comparative genomic analyses aimed at exploring its metabolic functions and conducting safety assessments are still lacking. Methods: In this study, we performed a comparative genomic analysis of 324 L. plantarum strains sourced from various origins and geographical locations. Results: The results revealed that L. plantarum possesses a total of 2403 core genes, of which 12.3% have an unknown function. The phylogenetic analysis revealed a mixed distribution from various origins, suggesting complex transmission pathways. The metabolic analysis demonstrated that L. plantarum strains can produce several beneficial metabolites, including lysine, acetate, and riboflavin. Furthermore, L. plantarum is highly capable of degrading various carbohydrates and proteins, increasing its adaptability. Further, we profiled the antimicrobial peptides (AMPs) in the genomes of L. plantarum. We identified a widely distributed AMP and its variants, presenting in a total of 280 genomes. In our biosafety assessment of L. plantarum, we identified several antibiotic resistance genes, such as Tet(M), ANT(6)-Ia, and mdeA, which may have potential for horizontal gene transfer within the Lactobacillaceae family. Conclusions: This study provides genomic insights into the genetic diversity, metabolic functions, antimicrobial properties, and biosafety of L. plantarum, underscoring its potential applications in biotechnology and environmental adaptation. Full article

Enteric diseases represent one of the main causes of morbidity and mortality in poultry production, especially in turkeys (Meleagris gallopavo), significantly affecting the profitability of the sector. Turkey enteric complex (PEC) is a multifactorial syndrome characterized by diarrhea, stunting, poor feed conversion, and increased mortality in young turkeys. Its aetiologia includes multiple avian enteric viruses, including astrovirus, rotavirus, reovirus, parvovirus, adenovirus, and coronavirus, which can act singly or in co-infection, increasing clinical severity. This study performs a systematic review of the literature on these viruses and a meta-analysis of their prevalence in different regions of the world. Phylogenetic analyses were used to assess the genetic diversity of the main viruses and their geographical distribution. The results show a wide regional and genetic variability, which underlines the need for continuous epidemiological surveillance. Health and production implications are discussed, proposing control strategies based on biosecurity, targeted vaccination, and optimized nutrition. These findings highlight the importance of integrated management to mitigate the impact of CSF in poultry. Full article

To explore the dyeing technique and karyotype analysis of winter turnip rape (Brassica rape L.), the root tip of winter turnip rape Longyou 7 was used as the experimental material. Chromosome preparation technology was optimized, and karyotype analysis was carried out by changing the conditions of material collection time, pretreatment, fixation, and dissociation. The results showed that the optimal conditions for the preparation of dyeing winter turnip rape were as follows: the sampling time was 8:00–10:00, the ice–water mixture was pretreated at 4 °C for 20 h, the Carnot’s fixative solution I and 4 °C were fixed for 12 h, and the 1 mol/L HCl solution was bathed in a water bath at 60 °C for 10~15 min. Karyotype analysis showed that the number of chromosomes in winter turnip rape cells was 2n = 20, and the karyotype analysis formula was 2n = 2x = 20 = 16m + 4sm. The karyotype asymmetry coefficient was 58.85%, and the karyotype type belonged to type 2A, which may belong to the primitive type in terms of evolution. The results of this study provide a theoretical basis for further in-depth study of the phylogenetic evolution and genetic trend of Brassica rapa. Full article

Scavenging domestic ducks significantly contribute to the transmission and maintenance of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses in Bangladesh, a strain of growing global concern due to its broad host range, high pathogenicity, and spillover potential. This study investigates the molecular epidemiology and pathology of HPAI H5N1 viruses in unvaccinated scavenging ducks in Bangladesh, with the goal of assessing viral evolution and associated disease outcomes. Between June 2022 and March 2024, 40 scavenging duck flocks were investigated for HPAI outbreaks. Active HPAIV H5N1 infection was detected in 35% (14/40) of the flocks using RT-qPCR. Affected ducks exhibited clinical signs of incoordination, torticollis, and paralysis. Pathological examination revealed prominent meningoencephalitis, encephalopathy and encephalomalacia, along with widespread lesions in the trachea, lungs, liver, and spleen, indicative of systemic HPAIV infection. A phylogenetic analysis of full-genome sequences confirmed the continued circulation of clade 2.3.2.1a genotype G2 in these ducks. Notably, two samples of 2022 and 2023 harbored HPAIV H5N1 of clade 2.3.4.4b, showing genetic similarity to H5N1 strains circulating in Korea and Vietnam. A mutation analysis of the HA protein in clade 2.3.4.4b viruses revealed key substitutions, including T156A (loss of an N-linked glycosylation site), S141P (antigenic site A), and E193R/K (receptor-binding pocket), indicating potential antigenic drift and receptor-binding adaptation compared to clade 2.3.2.1a. The emergence of clade 2.3.4.4b with the first report of neurological and systemic lesions suggests ongoing viral evolution with increased pathogenic potential for ducks. These findings highlight the urgent need for enhanced surveillance and biosecurity to control HPAI spread in Bangladesh. Full article

Leeches hold significant medical and pharmaceutical value for antithrombotic treatments, yet their genetic diversity patterns remain poorly understood. We performed population genetic analyses on seven Hirudinaria manillensis populations from southern China using mitochondrial protein-coding genes (MitPCGs). Complete sequences of all 13 MitPCGs were obtained from 74 individuals. Haplotype diversity exhibited a logarithmic relationship with the gene length (R² = 0.858, p < 0.001), while nucleotide diversity showed a near-perfect alternating low-high pattern (Z = 2.938, p = 0.003). Concatenated sequence analyses indicated high haplotype diversity (>0.5) and low nucleotide diversity (<0.005) across all populations, suggesting a historical bottleneck followed by rapid expansion and mutation accumulation. The haplotype network, haplotype phylogenetics, and genetic structure analyses revealed moderate genetic differentiation across populations, dividing them into three clades: a basal Yunnan population (YNHH), sub-basal Guangxi populations (GXGG, GXLZ, and GXYL), and distal Guangdong/Hainan populations (GDMM, GDZJ, and HNDA). Analysis of historical population demography revealed five phases from ancient to recent times (P1–5): growth, prolonged stability, rapid decline, rapid growth, and secondary decline. These phases correlate strongly with past climatic events, demonstrating that glacial–interglacial cycles profoundly impacted the leech’s effective population size. This study provides a key scientific basis for H. manillensis resource conservation and utilization. Full article

Tripterygium wilfordii has extremely important pharmaceutical value in both traditional and modern medicine. The mitogenome of T. wilfordii was subjected to assembly and annotation with Nanopore long reads and Illumina short reads in this study. The mitogenome is 720,306 bp in length and is responsible for encoding 55 specific genes, including 35 protein-coding genes (PCGs), 17 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Upon repetitive sequence analysis, 223 simple sequence repeats (SSRs), 24 long tandem repeats (LTRs), and 47 dispersed repetitive sequences (DRSs) were identified. The 24 common PCGs were used for phylogenetic analysis, which revealed that T. wilfordii is more closely related to Euonymus alatus. Moreover, mitochondrial plastid DNA (MTPT) analysis revealed eight MTPTs in the mitochondrial genome. Furthermore, 600 RNA-editing sites were detected in the protein-coding genes according to RNA-seq results. Among these genes, the ccmB gene contained the greatest number of sites, followed by the nad4 gene. This is the first study to report the T. wilfordii mitogenome and illustrate its linear structure. The findings of this study will help elucidate the evolution of the T. wilfordii mitogenome and facilitate its potential application in genetic breeding. Full article