Search Results (60)

Buds are continuously renewed sensory organs in which development, adult maintenance, and repair share overlapping molecular circuitry. During embryogenesis, WNT/β-catenin signaling promotes taste placode formation and placodal Shh expression, while SHH refines papilla spacing and restricts neighboring papilla formation. SOX2 functions as a taste-competence and progenitor maintenance factor. In adults, LGR5/LGR6–RSPO–WNT signaling sustains progenitor activity, and gustatory neurons are an important source of RSPO2; available genetic evidence is consistent with a neuron-derived contribution to the LGR5/LGR6 niche, and AAV-Cre-mediated neuron-specific ablation of Rspo2 in the petrosal ganglion led to near-complete loss of circumvallate taste buds. HH signaling from epithelial and neuronal sources further supports SOX2-dependent progenitor homeostasis. Lineage allocation is governed by transcriptional programs that include POU2F3/SKN-1a for sweet, umami, and bitter type II taste receptor cells, and ASCL1 with posterior-field NKX2-2 for type III presynaptic/sour cells. After denervation or irradiation, regeneration depends primarily on LGR5⁺/KRT14⁺ progenitors and may be supplemented, in specific injury contexts, by plasticity of a subset of K8-lineage taste receptor cells that acquire KRT14/SOX2/PCNA progenitor-like features. Key unresolved questions include the direct chromatin targets of taste lineage regulators (which remain to be defined by ChIP-seq in native taste progenitors), the identity of the type I cell selector, the contribution of dedifferentiation across injury models, and the degree to which mouse-derived networks are conserved in human taste biology. Full article

The floodplains of the Paraná and Paraguay rivers form the Chaco wetland, one of the most species-rich plant ecosystems in Argentina. Because wild grasses can serve as reservoirs of fungal species that cause disease and mycotoxin contamination of cereal crops, we examined asymptomatic, wild grasses from the Chaco wetlands for the presence of the genus Fusarium, which includes multiple species that cause agriculturally important diseases and/or mycotoxin contamination of crops. We focused our efforts on the identification and characterization of the multispecies lineage known as the Fusarium fujikuroi species complex (FFSC). Using morphological traits and partial DNA sequences of the TEF1 gene, we determined that 58 isolates recovered from the grasses were members of FFSC. Fifty of the isolates were identified as one of six FFSC species, including the economically important plant pathogenic species F. proliferatum, F. subglutinans, and F. verticillioides. To our knowledge, two of the species, F. anthophilum and F. pseudocircinatum, have not been reported previously in Argentina. Our analyses also indicated that eight of the FFSC isolates were a novel species, herein described as Fusarium varsavskyanum. A polymerase chain reaction (PCR) assay and genome sequence data indicate that each isolate of F. varsavskyanum isolate had only one mating type idiomorph (MAT1-1 or MAT1-2), which suggests that the fungus is heterothallic. Genome sequence analysis indicated that F. varsavskyanum has the genetic potential to produce, (i) the emerging mycotoxins fusaric acid and beauvericin (or enniatins); (ii) the pigments bikaverin, carotenoids, and fusarubin; and (iii) the plant hormones auxins, cytokinins, and gibberellins. Thus, asymptomatic grasses from the Chaco wetland can harbor Fusarium species that in some agroecosystems can cause economically important diseases and/or mycotoxin contamination of crops. It remains to be determined whether the genotypes of Fusarium species that occur on the wetland grasses, including F. varsavskyanum genotypes, can negatively impact agriculture. Full article

Rotavirus A (RVA) G3P[3] genotype is widely reported in dogs and less frequently in cats, with only sporadic human cases worldwide. All reported human infections have occurred in children, suggesting increased susceptibility likely linked to close contact with pets and age-related hygiene practices. The identification of a novel genotype constellation in Brazilian canine G3P[3] strains in 2017 prompted full-genotype characterization of the historical RVA/Human-wt/BRA/IAL-R451/2011/G3P[3] strain, previously sequenced only for VP7 and VP4, to define its genomic constellation and relatedness to canine strains. All 11 segments were analyzed by RT-PCR, sequencing and phylogenetics. The rare genotype–lineage constellation G3.III-P[3]-I2.XX-R3.II-C2.V-M3.II-A9-N2.XXIV-T3.II-E3.II-H6.I, shared with Brazilian canine strains, was identified, supporting a potential common origin. RVA/Human-wt/BRA/IAL-R451/2011/G3P[3] strain showed high genetic similarity (93.2–99%) with canine, feline and canine/feline-like human strains worldwide, with six genes (VP1, VP6 and NSP2–NSP5) closely related to Brazilian dog isolates (97.6–99%), indicating its canine origin. NSP2 clustered with strains from domestic (bovine), synanthropic (rat) and human hosts, while VP7 and VP4 were associated with wildlife (bat; raccoon dog) and environmental (sewage; river water) strains, supporting interhost reassortment and highlighting aquatic environments as reservoirs for interspecies transmission. Identification of new lineages (VP1, VP3 and NSP2) within the AU-1-like backbone reflects its underexplored diversity. This novel constellation likely circulated in dogs and may spill over to humans via close contact, reinforcing a One Health approach to understand RVA zoonotic risk, especially in hotspot regions like Brazil. Full article

Deep-sea hydrothermal vent fauna is often regarded as highly endemic, although exceptions have been reported. We examined genetic connectivity across broad spatial scales within the alvinocaridid genus Rimicaris, which has undergone substantial adaptive radiation worldwide. We analyzed six Rimicaris species using three genetic markers, cytochrome c oxidase subunit I (COI), 16S ribosomal rRNA gene (16S), and histone h3 (H3), and complete mitogenomes, employing newly generated sequences combined with publicly available sequence data. A genetic tree and haplotype networks were constructed, and divergence analyses were performed. Three clades of paired Rimicaris species were identified, each made up of taxa from different oceanic regions but showing relatively low COI divergence (0.35–1.90%). In Clade I, Rimicaris chacei and Rimicaris hybisae are morphologically similar and exhibit bidirectional gene flow, implying a dispersal route between the Mid-Atlantic Ridge (MAR) and the Mid-Cayman Spreading Center (MCSC). In Clade II, Rimicaris exoculata and Rimicaris kairei are morphologically, genetically, and ecologically distinct, reflecting restricted connectivity between the MAR and the Carlsberg Ridge (CR)–Central Indian Ridge (CIR). In Clade III, Rimicaris variabilis and Rimicaris cf. variabilis differ in nutritional strategies, showing a unidirectional dispersal route from the CIR to the southwestern Pacific (SWP), but morphological data to distinguish them are currently lacking. Some Rimicaris lineages maintain connectivity across distinct oceanic regions while others still form unique regional populations. This finding highlights the need for conservation strategies that incorporate both global-scale connectivity and regional endemism, rather than treating individual vent ecosystems as a single homogeneous management unit. Full article

Background: Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) remains a significant threat to swine production globally, including Japan. While the genetic diversity of PRRSV-2 has been reported previously, the potential association with modified live vaccines (MLVs) is not well understood. This study aimed to characterize PRRSV-2 strains currently circulating in Japan and assess possible links with MLVs. Methods: A total of 1190-nucleotide open reading frame 5 sequences of PRRSV-2 were collected across Japan between 2020 and 2023, and phylogenetic analyses were performed to classify genetic clusters. Additionally, correlations between cluster distribution and MLV usage were examined, using sequences detected in the Kanto region. Results: Phylogenetic analysis revealed that 48.5% of the sequences belonged to Cluster III, with a median nucleotide identity of 88.2% to the Japanese reference strain EDRD-1. Notably, the sequence identity between the strains detected in this study and EDRD-1 was significantly lower than that of strains identified in 1992–1993 (p < 0.05). In the Kanto region, Cluster I and II variants, which exhibited high sequence homology to MLV strains, were exclusively detected on farms with a history of MLV usage. Furthermore, Cluster IV displayed substantial genetic divergence, suggesting it comprises a heterogeneous group of distinct lineages. Conclusions: These findings demonstrated the temporal changes in the genetic diversity of Cluster III and provided suggestions of a possible influence that MLV usage influences PRRSV-2 cluster distribution, with Clusters I and II likely representing vaccine-origin viruses. The marked heterogeneity of Cluster IV also highlights the limitations of the current cluster-based classification. Full article

Paulownia trees are grown globally for their robust timber, agroforestry, and effective carbon dioxide drawdown. China possesses rich Paulownia germplasm resources, offering favorable material for the genetic improvement. Understanding the taxonomy and phylogenetic relationships of Paulownia species is essential for the advancement of germplasm innovation. In this study, we re-sequenced 67 typical accessions of 11 species within the Paulownia genus. A total of 16,163,790 high-quality single nucleotide polymorphisms (SNPs) were identified. Based on these markers, these accessions were classified into three groups: P. fortunei and P. lampropylla (Group I); P. tomentosa, P. fargesii, and P. kawakamii (Group II); and P. taiwaniana, P. jianshiensis, P. catalpifolia, P. elongata, P. ichangensis, and P. albiphloea (Group III). Using maximum likelihood estimation, population genetic structure analysis revealed that the 11 species originated from four different ancestral populations. The two predominant breeding species—P. fortunei and P. tomentosa—exhibit divergent origins: P. fortunei arose from hybridization between two ancestral species followed by complex admixture, whereas P. tomentosa retains a predominantly singular ancestral lineage, with traces of P. kawakamii. The genetic diversity (π) of P. tomentosa was 0.002588, which was considerably lower than that of P. fortunei (0.004181) suggesting that P. tomentosa is subjected to a stronger breeding selection during the evolution than P. fortunei. A total of 59 selected regions and 65 genes were identified by selective sweep analysis. These genes may be involved in biological processes such as morphological development and response to abiotic stress and hormonal activity regulation. These findings provide valuable references for further research on the genetic differentiation and adaptive evolutionary mechanisms of Paulownia species, laying a foundation for future germplasm innovation and variety improvement. Full article

Camphora officinarum Nees constitutes a pivotal tree species within the evergreen broad-leaved forests of East Asia, endowed with significant economic, ornamental, and ecological importance. Nevertheless, previous research has markedly underestimated the genetic diversity of this species, thereby hindering our efforts in conserving resources and enhancing genetic breeding. The current study generated 155 chloroplast genomes from specimens of C. officinarum obtained from six provinces/regions in China. The results reveal the identification of seven distinct clades (I–VII), with Clades II, III, V, and VII exhibiting genome expansions, primarily influenced by lineage-specific elongation of inverted repeats (IRs), whereas Clades I, IV, and VI maintained conserved IR lengths. Despite the structural plasticity, the GC content remained highly conserved. Geographic patterns indicated gene flow between adjacent regions (e.g., Hunan and Hubei with identical IR lengths), but genetic isolation in Fujian. High-polymorphism regions (psba-matK, ycf1, ycf2, and ndhF) were identified as superior phylogenetic markers, enhancing intraspecies-level resolution. Simple sequence repeats (SSRs) varied significantly among clades, dominated by A/T-rich mononucleotide repeats. These repeats, along with divergent repeat types (e.g., absence of reverse repeats in Clades V/VI), serve as robust tools for resource identification and evolutionary trajectory inference. Phylogenetically, samples from Fujian formed a distinct lineage, while samples from other regions, especially Guangdong, were mixed, with this finding probably being a reflection of historical cultivation and anthropogenic translocation. This study offers a framework for the genetic breeding and investigation of the evolutionary history of C. officinarum. Full article

While a global downward trend in rotavirus diarrhea cases has been observed following vaccine introduction, reassortment, genetic drift, and vaccine-escaping strains remain a concern, particularly in Sub-Saharan Africa. Here, we provide genomic insights into three equine-like G3P[8] rotavirus strains detected in Benin during the post-vaccine era. Whole-genome sequencing was performed using the Illumina MiSeq platform, and genomic analysis was conducted using bioinformatics tools. The G3 of the study strains clustered within the recently described lineage IX, alongside the human-derived equine-like strain D388. The P[8] is grouped within the lineage III, along with cognate strains from the GenBank database. Both the structural and non-structural gene segments of these study strains exhibited genetic diversity, highlighting the ongoing evolution of circulating strains. Notably, we identified a novel NSP2 lineage, designated NSP2-lineage VI. Amino acid comparisons of the G3 gene showed two conservative substitutions at positions 156 (A156V) and 260 (I260V) and one radical substitution at position 250 (K250E) relative to the prototype equine-like strain D388, the equine strain Erv105, and other non-equine-like strains. In the P[8] gene, three conservative (N195G, N195D, N113D) and one radical (D133N) substitutions were observed when compared with vaccine strains Rotarix and RotaTeq. These findings suggest continuous viral evolution, potentially driven by vaccine pressure. Ongoing genomic surveillance is essential to monitor genotype shifts as part of the efforts to evaluate the impact of emerging strains and to assess vaccine effectiveness in Sub-Saharan Africa. Full article

The history of the rabies virus dates back four millennia, with the virus being considered by many to be the first known transmitted between animals and humans. In Brazil, rabies virus variants associated with terrestrial wild animals, marmosets, and different bat species have been identified. In this study, bat samples from different regions of São Paulo State, in Southeast Brazil, were analyzed to identify their genetic variability and patterns. A total of 51 samples were collected over ten years (1999–2009) and submitted to the immunofluorescent technique using monoclonal antibodies for antigenic profile detection (the diagnostic routine used in Latin American countries) and genetic evolution analysis through maximum likelihood approaches. Three antigenic profiles were detected: one related to the rabies virus maintained by hematophagous bat populations (AgV3), part of the monoclonal antibody panel used, and two other profiles not included in the panel (called NC1 and NC2). These antigenic profiles were genetically distributed in five groups. Group I was related to hematophagous bats (AgV3), Groups II and III were related to insectivorous bats (NC1) and Groups IV and V were also related to insectivorous bats (NC2). The results presented herein show that genetic lineages previously restricted to the northwest region of São Paulo State are now found in other state regions, highlighting the need for a comprehensive genetic study of bat rabies covering geographic and temporal space, through expanded genomic analysis using a standard genomic fragment. Full article

Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial challenges from blast disease, yet our understanding of the genetic structure of M. oryzae populations in this region remains limited. Here, we analyzed 885 M. oryzae strains from 18 nurseries across four rice ecological regions in Southern China using a panel of genome-wide SNP markers. Phylogenetic and principal component analyses revealed three distinct clonal lineages: lineage I (58.19%), lineage II (21.36%), and lineage III (20.45%). Lineage I exhibited a broader geographic distribution compared to the other two lineages. Host-adapted divergence was observed across rice subspecies, with lineage III predominantly associated with japonica growing-regions, while lineages I and II mainly colonized indica rice-growing regions. Genetic diversity exhibited significant spatial heterogeneity, with the nucleotide diversity (π) ranging from 0.17 in South China to 0.32 in the Middle–Lower Yangtze River region, reflecting differential cropping systems. The predominantly negative Tajima’s D values across populations suggested recent expansion or selective sweeps, likely driven by host resistance pressures. High genetic differentiation between lineage I and other lineages contrasted with low divergence between lineages II and III, indicating distinct evolutionary trajectories. Furthermore, an uneven distribution of mating types among three genetic lineages was observed, suggesting limited sexual recombination within clonal lineages. The information obtained in this study may be beneficial in devising suitable strategies to control rice blast disease in Southern China. Full article

Tick-borne piroplasmids are apicomplexan protozoa that infect a wide range of vertebrate hosts, with significant implications for animal and human health. This study investigated the occurrence and genetic diversity of piroplasmids in wild mammals, unconventional pets, and associated ticks in Goiás state, midwestern Brazil. Between April 2023 and January 2024, 105 blood samples, 22 tissue samples, and 300 ticks were collected from 21 mammalian species housed in wildlife screening centers, zoos, and veterinary clinics. Molecular screening targeting the 18S rRNA gene of piroplasmids detected a 25.7% (27/105) overall positivity, with gray brockets (Subulo gouazoubira) and South American tapirs (Tapirus terrestris) showing the highest infection rates. Three tick samples tested positive, including two Amblyomma sculptum nymphs and a male of Amblyomma dubitatum collected from a tapir and capybara (Hydrochoerus hydrochaeris). Cytauxzoon brasiliensis was reported, for the first time, in cougars (Puma concolor) from Goiás state, midwestern Brazil, indicating the role of this feline as a host of this parasite. Babesia goianiaensis was confirmed in a capybara, and Theileria terrestris in tapirs. Phylogenetic analyses clustered gray brockets-associated Theileria sequences with Theileria sp. previously detected in Neotropical deer from Brazil and Theileria cervi. While the phylogenetic analysis of amino acid sequences of the cytochrome c oxidase subunit III separated Theileria genotypes detected in S. gouazoubira from T. cervi, hsp70-based phylogenetic inferences clustered the genotypes detected in Tapirus terrestris with Theileria terrestris, suggesting host-specific evolutionary lineages. These findings contribute to the understanding of Piroplasmida diversity and circulation in South American wild mammals, emphasizing the need for enhanced molecular surveillance to elucidate transmission dynamics, assess potential health risks, and contribute to the establishment of wildlife conservation and One Health strategies. Full article

Sargassum hemiphyllum var. chinense is a common brown seaweed along the southeastern coast of China, playing a significant ecological role and possessing considerable resource utilization value. However, its genetic diversity and phylogeographic patterns remain poorly understood. In this study, we employed multiple molecular markers, including the nuclear ITS sequence (ribosomal internal transcribed spacer), the plastid rbcL gene (encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase), and the mitochondrial cox3 and cox1 genes (encoding cytochrome c oxidase subunits III and I, respectively), to elucidate the genetic and phylogeographic structure of S. hemiphyllum var. chinense. Our findings demonstrate that the combined use of plastid and mitochondrial gene sequences is suitable for phylogeographic studies of this species. Genetic structure difference was observed among 15 populations which localities covering most of its distribution range, likely resulting from colonization by ancestors of different origins and limited gene flow among populations. The study revealed two distinct lineages of S. hemiphyllum var. chinense, exhibiting a north–south geographical distribution with a mixed zone in the southern Fujian–eastern Guangdong coastal region. These lineages are inferred to have diverged during the Middle to Late Pleistocene due to the isolation of the East China Sea and South China Sea during glacial periods. Sub-lineage differentiation was also detected within the northern lineage. The southern lineage experienced demographic expansion following the end of the Last Glacial Maximum, while the northern lineage remained stable. The southern Fujian–eastern Guangdong region, characterized by high genetic diversity, may have served as a glacial refugium or a contact zone for the post-glacial recolonization of the two lineages. Global warming may lead to range contraction and reduced genetic diversity in this species. The high genetic diversity area should be prioritized for conservation efforts. Overall, these findings provide insights into the genetic structure status and causes of S. hemiphyllum var. chinense and offer a scientific basis for proposing reasonable measures for its resource management. Full article

Southeast Asia’s biodiversity refugia, shaped by Neogene–Quaternary climatic shifts and the Tibetan Plateau uplift, preserve relict lineages like Exbucklandia (Hamamelidaceae). Once widespread across ancient continents, this genus now survives in Asian montane forests, offering insights into angiosperm diversification. Chloroplast haplotypes formed three clades—Clade I (E. tricuspis), Clade II (E. populnea), and Clade III (E. tonkinensis)—with E. longipetala haplotypes nested within II/III. Nuclear microsatellites (SSRs) identified two ancestral gene pools: E. populnea and E. tricuspis showed predominant ancestry in Pool A, while E. tonkinensis and E. longipetala were primarily assigned to Pool B. All taxa exhibited localized genetic admixture, particularly in sympatric zones. Divergence dating traced the genus’ origin to tropical Asia, with northward colonization of subtropical China ~7 Ma yielding E. populnea and E. tonkinensis. Quaternary Glacial Cycles triggered southward expansions, chloroplast capture, and localized hybridization. Morphological, nuclear, and plastid molecular evidence supports reclassifying E. longipetala as E. populnea × E. tonkinensis hybrids lacking genetic cohesion and E. tricuspis as a distinct species with a mixed nuclear composition. This study highlights how paleoclimate-driven gene flow shaped the phylogeography of relict taxa in Southeast Asia and the urgency of habitat restoration to conserve Exbucklandia. Full article

Dengue fever remains a significant public health concern in tropical regions, including Central India, where outbreaks are frequent and associated with high morbidity and mortality. This study investigated the dynamics of dengue virus transmission and evolution in Central India from 2019 to 2023, focusing on the emergence of new strains and their impact on outbreak patterns. For this, 40 mosquito pools and 300 patient samples were recruited for the study. Phylogenetic and Bayesian evolutionary analyses performed on CPrM region and whole genome sequences generated by Sanger and Illumina sequencing, respectively, revealed the emergence and predominance of a novel DENV-2 genotype IV lineage III strain in the 2019 and 2023 outbreaks, which displaced the previously circulating DENV-1 genotype responsible for the 2016–2017 outbreak. Despite pre-existing DENV-1 neutralizing antibodies in the community (67 healthy volunteers), the novel DENV-2 strain exhibited higher viral loads and a greater reproduction number (R0), contributing to rapid disease spread. Molecular clock and Shannon entropy analyses suggest that DENV evolution occurred within the mosquito vector, driven by natural selection. Our findings highlight the importance of continuous DENV surveillance, including genetic characterization in both vectors and hosts, to understand viral evolution and predict future outbreaks. Rapid urbanization and inadequate sanitation in densely populated regions like India create ideal breeding grounds for mosquitoes, facilitating the introduction and establishment of novel DENV strains. Interrupting the vector–DENV–host cycle through targeted interventions is crucial for effective dengue control. Full article

Background/Objective: The anti-restriction protein ArdA-H1, found in multiresistant Staphylococcus aureus (MRSA) strains from the ST239-SCCmecIII lineage, inhibits restriction–modification systems, fostering horizontal gene transfer (HGT) and supporting genetic adaptability and resistance. This study investigates the regulatory mechanisms controlling ardA-H1 expression in S. aureus under various stress conditions, including acidic pH, iron limitation, and vancomycin exposure, and explores the roles of the Agr quorum sensing system. Methods: The expression of ardA-H1 was analyzed in S. aureus strains exposed to environmental stressors using real-time quantitative reverse transcription PCR. Comparisons were made between Agr-functional and Agr-deficient strains. In addition, Agr inhibition was achieved using a heterologous Agr autoinducing peptide. Results: The Agr system upregulated ardA-H1 expression in acidic and iron-limited conditions. However, vancomycin induced ardA-H1 activation specifically in the Agr-deficient strain GV69, indicating that an alternative regulatory pathway controls ardA-H1 expression in the absence of agr. The vancomycin response in GV69 suggests that diminished quorum sensing may offer a survival advantage by promoting persistence and HGT-related adaptability. Conclusion: Overall, our findings provide new insights into the intricate relationships between quorum-sensing, stress responses, bacterial virulence, and genetic plasticity, enhancing our understanding of S. aureus adaptability in challenging environments. Full article