Search Results (3,597)

The Jialing River is a representative and typical canalized tributary in the upper Yangtze River basin. In the context of the 10-year fishing ban, it is imperative to elucidate the dynamics and assembly of fish communities in the Jialing River. In this study, field surveys were conducted during the flood and dry seasons from 2021 to 2025 at the Cangxi section of the Jialing River. Fifty fish species belonging to three orders and six families were collected in the study area, with Chanodichthys oxycephaloides, Hemibarbus labeo, Xenocypris davidi, and Siniperca chuatsi identified as dominant species. In addition, fish communities in this region exhibited significant temporal variations, clustering into flood season and dry season groups (p < 0.05). The result suggested that diversity indices were consistently higher in the flood season than the dry season and an increasing trend was observed during the sampling periods. Community assembly analysis revealed that the fish communities were mainly characterized by phylogenetic clustered structure, indicating environmental filtering as the deterministic process in the study area. Despite the steady recovery of fish biodiversity and resource following the fishing ban in the study area, further attention must be directed to other anthropogenic disturbances, especially habitat fragmentation. This study provides a scientific reference for fisheries management after the fishing ban in the Jialing River. Full article

Apricot (Prunus armeniaca L.) exhibits a gametophytic self-incompatibility (GSI) system. To identify the S-genotypes of the main apricot cultivars, including 133 native Chinese cultivars and 35 foreign accessions, PCR was performed using a combination of five primers based on the conserved regions of Prunus S-RNase genes. After cloning and sequencing the PCR products, the S-genotypes of all 168 apricot cultivars were determined. A total of 46 different S-RNase alleles, with 15 new alleles, were identified. For all 168 accessions, the top five most frequent S-alleles were S₈, S₁₁, S₉, S₁₆, and S₅₃. S₁₁, S₈, and S₁₆ were the most frequent in Chinese cultivars, and S₉, S₈, and S₂ were mostly found in European accessions. For Chinese apricot cultivars, the distribution of S-alleles among five geographic regions was also investigated. In Northwest China, S₁₆ was the most frequent S-allele. In the Xinjiang region, S₆₆, S₄₉, and S₁₄ were the top three most frequent S-alleles. In North China, S₈, S₁₁, and S₅₃ were the top three most frequent S-alleles. In addition, the self-compatible type, S_C, was not detected in these 133 Chinese accessions. Finally, the phylogenetic tree of apricot S-alleles indicated that there are four groups of S-RNase genes (S₉₇/S₁₀₆, S₁₄/S_14a/S₆₆, S₉/S₁₇/S₄₄, and S₂₃/S₅₃) presenting a very close relation. These results provide more data on the S-genotypes of apricot accessions, which can support future breeding programs by aiding in the selection of the appropriate parents and contributing to efficient orchard design by combining cultivars with suitable pollinizers. Full article

Trochoidea caroni (Gastropoda, Geomitridae) is a land snail previously found only in Sicily and Capri (Naples), but it has recently been found in other regions of the Italian peninsula. In this study, we performed karyological and molecular analysis on T. caroni from different sites across this regional range. Karyological analysis was performed on specimens from Palermo (Sicily), Capri (Campania), and Terracina (Lazio) using standard staining and NOR-FISH methods; the latter method was also performed on samples of T. elegans from Rome (Lazio). All T. caroni specimens had 2n = 48 chromosomes, but the 8th and 17th pairs differed morphologically between specimens from Capri and Terracina and those from Sicily. The mitochondrial 16S rRNA analysis grouped Sicilian and non-Sicilian populations of T. caroni in distinct subclades. Superimposing karyological data on their phylogenetic tree suggests that possible chromosomal rearrangements occurred during the diversification of Trochoidea. Our findings provide karyological and molecular evidence for a diversification between Sicilian and non-Sicilian populations of T. caroni. Furthermore, NOR-FISH revealed hybridisation signals on the 16th chromosome pair in both T. caroni and T. elegans (tribe Trochoideini). Similar NOR localisation has also been identified in Cernuella virgata (tribe Cernuellini), suggesting that it was inherited from the common ancestor of Trochoideini and Cernuellini. Full article

Plant respiratory burst oxidase homolog (Rboh) genes are integral to the production of reactive oxygen species (ROS) and the regulation of stress responses. Here, bioinformatic techniques were employed to identify eight PgRboh genes (PgRbohA–H) in the genome of pomegranate (Punica granatum L.) and conduct a systematic analysis of this family. The findings showed that all PgRbohs proteins possess characteristic NADPH oxidase domains and are predicted to be localized on the cell membrane. Experimental verification confirmed the membrane localization of PgRbohD and PgRbohE proteins. Phylogenetic analysis categorized the PgRbohs proteins into six distinct groups, suggesting potential functional divergence among these groups. Promoter analysis revealed a significant presence of cis-acting elements responsive to low-temperature and methyl jasmonate (MeJA). The expression of PgRboh genes was found to be tissue-specific. Additionally, real-time PCR (RT-qPCR) was used to analyze expression patterns in response to low-temperature stress that involves multiple PgRboh genes in the cold response process. Overall, our results lay an important foundation for subsequent studies on the cold resistance function of pomegranate Rboh genes and provides new ideas for the breeding of new cold-resistant pomegranate varieties. Full article

In this paper, we use molecular phylogenetics, micro-CT scanning, and morphological analyses to describe a new species of goby, Pascua marecoralliensis, and demonstrate that the genus Pascua is distinct from Hetereleotris, as supported by five diagnostic characters, including modified basicaudal scales and reduced sensory papillae patterns. Phylogenetic analysis places Pascua as sister to the Gobiodon group, while Hetereleotris forms a separate clade. The new species, P. marecoralliensis, differs from congeners in fin ray counts, cephalic pore patterns, and head morphology and exhibits unique live colouration. Additionally, we reclassify Hetereleotris readerae and H. sticta as Pascua readerae and P. sticta based on shared genus-specific traits. The distribution of Pascua spans the southern Pacific, suggesting a relict lineage or undiscovered diversity in the genus. This work underscores the importance of integrative taxonomic approaches for resolving cryptic diversity in gobioid fishes and highlights the need for further sampling in understudied regions. Full article

The pan-plastome approach provides a powerful tool for investigating intraspecific divergence and population genetics due to its unique advantages, including single-copy genes, absence of recombination, and moderate nucleotide substitution rates. Adenocaulon himalaicum Edgew. (Asteraceae), a widely distributed medicinal herb in East Asia, remains genomically understudied at the population level, with no comprehensive pan-plastome assembly available to date. Here, we de novo assembled pan-plastome of 87 individuals from 18 populations representing its known distribution range. The pan-plastome exhibited a typical quadripartite structure (152,129 bp to 152,207 bp), containing 113 unique genes, most of which were under purifying selection. Phylogenetic and haplotypes analyses revealed three distinct genetic lineages corresponding to their geographic distribution. Population genetic analyses showed significant differentiation among three genetic groups (AMOVA: 73.43% variation among groups) and a strong isolation-by-distance pattern (IBD: r = 0.469, p = 0.001). The pronounced population structure underscores the imperative for establishing distinct conservation units, with particular emphasis on marginal populations that may harbor unique genetic compositions and potential medicinal properties. Our study presents the first pan-plastome for A. himalaicum, offering new insights into its plastome evolution and population divergence, providing valuable genomic resources to guide future breeding and sustainable utilization of medicinal herbs. Full article

Thanks to its ethological and physiological characteristics, the hedgehog is a synanthropic species of particular importance for the maintenance and possible spread of pathogens, some of which are zoonotic. Among these, we can include the mammalian orthoreovirus (MRV), which is characterized by respiratory, gastrointestinal, and neurological symptoms in both animals and humans. MRV is characterized by a high capacity for genetic reassortment and intragenic rearrangement, and the ability to infect a wide range of mammals. This work aims to investigate the presence of MRVs and its genomic characterization in hedgehogs. During the two-year period from 2022 to 2023, the intestine and lungs were collected from 293 hedgehogs and subjected to real-time PCR to detect the L1 gene. Positive samples were subjected to a typing RT-PCR targeting a portion of the S1 gene and then to sequencing. A total of 38 hedgehogs tested positive by real-time PCR (p = 13%). Typing RT-PCR demonstrated the positivity of 25 samples for serotype 3. Four samples, representative of the main groups recognized during the phylogenetic analysis, underwent whole genome sequencing, revealing the presence of reassortment phenomena between strains related to bats, chamois, and human MRVs. Full article

Staphylococcus aureus is an opportunistic pathogen, a member of the ESKAPE group, associated with nosocomial infections and foodborne illnesses due to its production of various toxins. This study conducted a comprehensive genomic characterization of S. aureus isolates producing toxic shock syndrome toxin (TSST-1) using a comparative genomics and bioinformatics approach. A total of 166, including 3 bovine mastitis isolates and 163 public genomes, were analyzed. Twenty-eight distinct sequence types (STs) were identified, with ST30 and ST5 being the most prevalent, corresponding to the clonal complexes CC30 and CC5, respectively. Phylogenetic reconstruction revealed two major clades aligned with these complexes, each exhibiting unique virulence factor profiles. Notably, TSST-1 was detected in bovine mastitis genomes, alongside a broad repertoire of virulence markers, such as enterotoxins and secretion system components, posing a potential risk to public health. Additionally, genes related to environmental information processing systems, including ABC transporters and phosphotransferase systems, were prevalent. These results underscore the need for strengthened genomic surveillance and the implementation of both preventive and corrective measures in dairy herds to mitigate zoonotic transmission and ensure food safety. Full article

Bristletails (Microcoryphia) represent a relatively understudied group of class Insecta. These wingless hexapods, which retain numerous plesiomorphic structures, remain less well understood compared to most other insect lineages. Through detailed morphological examination of specimens collected from southern China, we describe six new species (Pedetontus (Verhoeffilis) elegans sp. n. from Zhejiang; P. (V.) hezhouensis sp. n., P. (V.) jinxiuensis sp. n., and P. (V.) nanningensis sp. n. from Guangxi; and P. (V.) shenzhenensis sp. n. and P. (V.) xanthospilus sp. n. from Guangdong) of subgenus Verhoeffilis Paclt, 1972. This subgenus is distinguished from other members of the Petrobiinae by several diagnostic features: paired ocelli shoe-shaped (fusiform-shaped) and submedian; two pairs of retractile vesicles on abdominal segments II–V; parameres restricted to coxite IX; penis opening small and apical; male genitalia not exceeding coxite IX; and ovipositor of primary type. The new species can be distinguished from known species and each other by the morphology of the compound eyes, maxilla, labial palps, legs, and genitalia; here, we provide detailed illustrations, tables, and descriptions. Furthermore, we sequence the COX1 gene to construct a phylogenetic tree of Microcoryphia. This contribution increases the total number of reported Pedetontus species in China to seventeen. Full article

From January 2019 to April 2020, the Minnesota Veterinary Diagnostic Laboratory (MVDL) received cases of hepatitis and spiking mortality in young turkey poults (average age 15.5 days) from multiple turkey-producing states. Meat-type turkeys were mainly affected, with a few cases in breeders. Of 188 cases, 88 (47.5%) tested positive for reovirus by virus isolation, with most of the positive cases from 7 to 14-day-old birds (n = 42). Gross lesions consisted of hepatosplenomegaly with acute, multifocal necrosis in both liver and spleen. Microscopically, liver sections showed congestion of hepatic sinusoids and necrotizing hepatitis with infiltration of lymphocytes, plasma cells, and macrophages. Reovirus was detected in liver samples by electron microscopy and in situ hybridization (ISH). Sections of spleen showed areas of necrosis with infiltration of the mixed population of inflammatory cells and depletion of lymphocytes. We consistently isolated reoviruses from livers and tentatively named the virus “Turkey Hepatitis Reovirus” (THRV). Phylogenetic analysis of the newly emerged THRVs revealed their clustering into four distinct groups. This study also highlighted the close antigenic relation between TARV and THRV compared to turkey enteritis reoviruses (TERVs), which shed light on the probable origin of this newly emerged pathotype. In summary, further molecular and pathogenicity studies are recommended on THRVs to help diagnose and control this serious variant. Full article

Human parainfluenza viruses 3 (hPIV3) are important pathogens, responsible for acute respiratory tract diseases, especially in young children. Information on hPIV3 circulation and their diversity pattern in Russia is limited. The aim of this study was to perform a molecular and genetic characterization of hPIV3 circulating in Saint Petersburg, Russia. From October 2017 to September 2023, 14,704 swabs were screened using real-time reverse transcription-PCR. A phylogenetic analysis of the complete hemagglutinin–neuraminidase (HN) gene was performed. Out of 1334 positive hPIV cases, hPIV3 was the most common subtype. Phylogenetic analysis of the studied and previously published HN sequences revealed four distinct genetic clusters, A, B, C, and D, with Cluster D being first delineated in this study. In addition, two newly subdivided genetic lineages, C5a and C5b, were documented. Phylogenetic analysis revealed that the analyzed Russian strains grouped into Cluster C and D; further subclusters C5a, C5b, C3b, C3e, and C3a. While three strains were classified within cluster D, the majority of isolates fell within subcluster C3a, followed by C5b. Taken together, these findings demonstrate the co-circulation of hPIV3 strains during the study period. This is the first study that describes the genetic and molecular aspects of hPIV3 circulating in Russia. Moreover, our results provide an up-to-date hPIV3 phylogenetic analysis. Full article

Southern tomato virus (STV) or Amalgavirus lycopersici is a persistent virus impacting tomato crops globally. This study identified new STV isolates from Oklahoma and analyzed their evolutionary relationship to global STV isolates. Phylogenetic analyses (complete genomes or individual genes) grouped STV isolates into two distinct clades, independent of geographic origin or host. Notably, Oklahoma isolates formed a separate cluster from previously reported isolates in the United States of America (USA). Coalescent analysis suggested the most recent common ancestor of STV fusion protein emerged around 135 years ago. Genetic diversity among STV isolates was low, with slightly more variability in the RNA-dependent RNA polymerase (RdRp) gene than the p42 gene. Both genes showed strong purifying selection. No recombination events were detected across complete genomes. Structure analysis revealed that the p42 protein, particularly its C-terminal region, displayed higher disorder, indicating a possible role in host interactions and viral adaptability. These findings deepen our understanding of STV’s evolution and highlight the need for ongoing surveillance and broader genomic sampling. Full article

B-box (BBX) transcription factors, which are specific to the plant kingdom, play a crucial role in regulating light-dependent growth, development, secondary metabolite biosynthesis, and the response to biotic and abiotic stresses. Despite their significance, there has been a lack of systematic investigation into the BBX gene family in Ginkgo biloba. In the present study, we identified nine BBX genes within the G. biloba reference genome, distributed across seven chromosomes, and classified them into four groups based on their phylogenetic relationships with the BBX gene families of Arabidopsis thaliana. Our analysis of gene structure, conserved domains, and motifs suggests that GbBBXs exhibit a high degree of conservation throughout evolutionary history. Additionally, synteny analysis revealed that dispersed duplication events have contributed to the expansion of the BBX gene family in G. biloba. An examination of cis-regulatory elements indicated that numerous GbBBX genes contain motifs associated with light, hormones, and stress, suggesting their potential roles in responding to these signals and environmental adaptation. Expression profiles obtained from RNA-Seq data and quantitative Real-Time PCR (qRT-PCR) analyses of GbBBX genes across various organs, hormone treatments, and leaves with differing flavonoid content, as well as during both short-term and long-term water stress, demonstrated their potential roles in flavonoid regulation and responses to hormones and water stress. Subcellular localization studies indicated that the proteins GbBBX5, GbBBX7, GbBBX8, and GbBBX9 are localized within the nucleus. This study is the first thorough analysis of the BBX gene family in G. biloba, providing a valuable foundation for further understanding their evolutionary context and functional roles in flavonoid regulation and responses to water stress. Full article

A major cause of lameness in turkeys is reoviral arthritis, driven by turkey reovirus (TRV) infection. In the U.S., TRV was first isolated in the 1980s but re-emerged as a significant pathogen causing arthritis in 2011. Since then, TRV outbreaks have spread nationwide across turkey-producing regions and have occasionally resulted in hepatitis-associated pathotypes. The absence of a consistently effective commercial vaccine continues to hinder disease control efforts. To better understand TRV’s evolutionary trajectory and transmission dynamics, we analyzed 211 complete TRV genome sequences collected across the U.S. from 2007 to 2021. Bayesian time-scaled phylogenetic and phylogeographic analyses were conducted for all ten genome segments to estimate gene flow among geographic regions, client groups, and pathotypes. The results reconstructed a coherent, decades-long history of TRV evolution, which revealed segment-specific differences in the evolutionary rates—particularly in S1c (σC protein coding region of S1) and M2—suggesting reassortment with other avian reoviruses during the 2011 emergence. Nationwide spread patterns indicated dominant transmission routes from the Eastern U.S. to Minnesota and from breeder to smallholder flocks, likely driven by inter-regional animal or feed movement via the multi-stage turkey production cycle. Pathotype transitions were more frequently observed from arthritis-associated strains to those causing hepatitis or cardiac lesions. These findings provide crucial insights to support national TRV control strategies and long-term monitoring by industry stakeholders. Full article

Background: Collabieae is a medium-sized group within the orchid subfamily Epidendroideae that is distributed primarily across tropical Asia. Most Collabieae species are known for their considerable ornamental and medicinal merits. However, habitat destruction and overharvesting have led to severe decline in their wild populations. Chloroplast (cp) genomes are highly valued in evolutionary studies, due to comparative conservation and accumulation of genomic variations. Elucidating the structure of chloroplast genome is instrumental in conserving genetic diversity within the Collabieae. Methods: we explored the chloroplast genome characteristics of Collabieae. We incorporated three newly sequenced genomes from species (Acanthophippium sylhetense, Eriodes barbata, and Spathoglottis plicata), along with seven related species. Results: all analyzed cp genomes displayed a typical quadripartite circular structure. The total lengths ranged from 157,036 bp to 158,321 bp. Each genome contained 136 genes: 88 protein-coding genes, 38 tRNA genes, eight rRNA genes, and two pseudogenes. Across the ten Collabieae species, gene number, order, orientation, GC content, and codon usage bias were highly consistent, indicative of strong sequence conservation. However, notable structural divergence was observed at the plastome junctions, alongside variations in SSR and repetitive element frequencies. Moreover, six hypervariable regions were identified. Noncoding regions exhibited higher variability compared to protein-coding regions. Phylogenetic analysis indicated that E. barbata forms a distinct, small branch sister to the rest of the Collabieae members. Genera Acanthophippium and Spathoglottis were sister to the remaining groups within the tribe. Conclusions: this overall phylogenetic framework aligns well with previous findings. Our study provides valuable cp genomic resources and advances evolutionary research in Collabieae. Full article