Complete mitochondrial genome of the common Pochard (Aythya ferina) from Ningxia Hui autonomous region, China.
Ontology highlight
ABSTRACT:
SUBMITTER: Zhai H
PROVIDER: S-EPMC8676666 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We determined the whole mtDNA genome of the gray-headed lapwing (Vanellus cinereus) in Ningxia Hui Autonomous Region, China. The complete mitochondrial genome is 17,078 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The nucleotide composition is 31.65% A, 23.50% T, 13.76% G, and 31.09% C. The result of phylogenetic analysis showed that there was close genetic relationship between V. cinereus and V. vanellus.
| S-EPMC7927989 | biostudies-literature
Project description:BackgroundNingxia Hui Autonomous Region is an important cattle breeding area in China, and cattle breeding bases are located in this area. In Ningxia, dermatophytes have not been paid attention to, so dermatophytosis is becoming more and more serious. For effective control measures, it is important to determine the disease prevalence and isolate and identify the pathogenic microorganism.ResultsThe study showed the prevalence of dermatophytes was 15.35% (74/482). The prevalence in calf was higher than adult cattle (p < 0.05). The morbidity was the highest in winter compared with autumn (p < 0.0001), summer (p < 0.05) and spring (p < 0.0001). The prevalence in Guyuan was the highest compared with Yinchuan (p < 0.05) and Shizuishan (p < 0.05). The incidence of lesions on the face, head, neck, trunk and whole body was 20.43, 38.71, 20.43, 10.75 and 9.68%, respectively. From all samples, the isolation rate of Trichophyton was highest (61.1%). The phylogenetic tree constructed showed that the 11 pathogenic fungi were on the same branch as Trichophyton verrucosum.ConclusionsThis study reports, for the first time, the presence of Trichophyton verrucosum in cattle in Ningxia and showed that the incidence of dermatophytosis is related to different regions, ages and seasons. A better knowledge of the prevalence of dermatophytosis of cattle may allow the adoption of more efficient control measures and prophylaxis.
| S-EPMC7288468 | biostudies-literature
Project description:ObjectiveThis study aimed to estimate the prevalence of hyperuricaemia (HUA) and investigate its risk factors in the general adult population of Ningxia Hui Autonomous Region (NHAR), China.DesignCross-sectional study.SettingSurvey of cardiovascular disorders and their related risk factors in NHAR, China.Participants10 803 permanent residents aged 18 and older.Main outcome measuresHUA was defined as serum uric acid levels >420 µmol/L for men and >360 µmol/L for women.ResultsThe overall prevalence of HUA in NHAR adults was 19.81% (95% CI 19.06 to 20.57), with prevalence values of 24.91% (95% CI 23.70 to 26.14) in men and 15.58% (95% CI 14.66 to 16.53, p<0.001) in women. The prevalence of HUA was higher in urban residents than in rural residents (23.26% vs 17.02%, p<0.001). HUA prevalence was relatively high in individuals younger than 30 years for both men and women, then decreased with age, and began to increase at the age of 40 for women and 60 for men. Higher level of education, being overweight or obese, alcohol consumption, hypertension, diabetes, higher triglycerides, higher total cholesterol and poorer renal function were associated with an increased risk of HUA.ConclusionsHUA prevalence is high among adults in NHAR. Young adults under 30 years and women over 50 years were identified as populations at high risk for HUA. Further attention ought to be placed to promoting healthy diets and implementing early interventions to manage dyslipidaemia, obesity and blood glucose level, as well as advocating for moderation of alcohol consumption.
| S-EPMC10603489 | biostudies-literature
Project description:The Ferruginous Duck (Aythya nyroca) is a diving duck that is widely distributed in Asia, Africa, and Europe. We determined the complete mitogenome of the Ferruginous Duck gathered at Ningxia, China. The total length of the complete mitochondrial genome is 16,623 bp and it consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 control region (CR). Only one overlap among the 13 protein-coding genes was found: ND4L/ND4. The CR is 1068 bp in length. The nucleotide composition is 29.66% A, 22.28% T, 15.35% G, 32.71% C. The result of phylogenetic analysis showed that there is close genetic relationship among Aythya nyroca and three ducks in the Genus Aythya.
| S-EPMC7889268 | biostudies-literature
Project description:BackgroundHuman cystic (CE) and alveolar (AE) echinococcoses are zoonotic parasitic diseases that can be influenced by environmental variability and change through effects on the parasites, animal intermediate and definitive hosts, and human populations. We aimed to assess and quantify the spatiotemporal patterns of human echinococcoses in Ningxia Hui Autonomous Region (NHAR), China between January 1994 and December 2013, and examine associations between these infections and indicators of environmental variability and change, including large-scale landscape regeneration undertaken by the Chinese authorities.MethodsData on the number of human echinococcosis cases were obtained from a hospital-based retrospective survey conducted in NHAR for the period 1 January 1994 through 31 December 2013. High-resolution imagery from Landsat 4/5-TM and 8-OLI was used to create single date land cover maps. Meteorological data were also collected for the period January 1980 to December 2013 to derive time series of bioclimatic variables. A Bayesian spatio-temporal conditional autoregressive model was used to quantify the relationship between annual cases of CE and AE and environmental variables.ResultsAnnual CE incidence demonstrated a negative temporal trend and was positively associated with winter mean temperature at a 10-year lag. There was also a significant, nonlinear effect of annual mean temperature at 13-year lag. The findings also revealed a negative association between AE incidence with temporal moving averages of bareland/artificial surface coverage and annual mean temperature calculated for the period 11-15 years before diagnosis and winter mean temperature for the period 0-4 years. Unlike CE risk, the selected environmental covariates accounted for some of the spatial variation in the risk of AE.ConclusionsThe present study contributes towards efforts to understand the role of environmental factors in determining the spatial heterogeneity of human echinococcoses. The identification of areas with high incidence of CE and AE may assist in the development and refinement of interventions for these diseases, and enhanced environmental change risk assessment.
| S-EPMC5824458 | biostudies-literature
Project description:Historically, the diving duck, Baer's Pochard (Aythya baeri) was widely distributed in East and South Asia, but according to a recent estimate, its global population is now less than 1000 individuals. To date, the mitochondrial genome of A. baeri has not been deposited and is not available in GenBank. Therefore, we aimed to sequence the complete mitochondrial genome of this species. The genome was 16,623 bp in length, double stranded, circular in shape, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. Many structural and compositional similarities were discovered between A. baeri and the other three Aythya mitochondrial genomes. Among 13 protein-coding genes of the four Aythya species, the fastest-evolving gene was ATP8 while the slowest-evolving gene was COII. Furthermore, the phylogenetic tree of Anatidae based on Bayesian inference and maximum likelihood methods showed that the relationships among 15 genera of the Anatidae family were as follows: Dendrocygna was an early diverging lineage that was fairly distant from the other ingroup taxa; Cygnus, Branta, and Anser were clustered into one branch that corresponded to the Anserinae subfamily; and Aythya, Asarcornis, Netta, Anas, Mareca, Mergus, Lophodytes, Bucephala, Tadorna, Cairina, and Aix were clustered into another branch that corresponded to the Anatinae subfamily. Our target species and three other Aythya species formed a monophyletic group. These results provide new mitogenomic information to support further phylogenetic and taxonomic studies and genetic conservation of Anatidae species.
| S-EPMC8692624 | biostudies-literature
Project description:Baer's pochard (Aythya baeri) is a critically endangered species historically widespread throughout East Asia, whose population according to a recent estimate has decreased to between 150 and 700 individuals, and faces a long-term risk of extinction. However, the lack of a reference genome limits the study of conservation management and molecular biology of this species. We therefore report the first high-quality genome assembly of Baer's pochard. The genome has a total length of 1.14 Gb with a scaffold N50 of 85,749,954 bp and a contig N50 of 29,098,202 bp. We anchored 97.88% of the scaffold sequences onto 35 chromosomes based on the Hi-C data. BUSCO assessment indicated that 97.00% of the highly conserved Aves genes were completely present in the genome assembly. Furthermore, a total of 157.06 Mb of repetitive sequences were identified and 18,581 protein-coding genes were predicted in the genome, of which 99.00% were functionally annotated. This genome will be useful for understanding Baer's pochard genetic diversity and facilitate the conservation planning of this species.
| S-EPMC10060409 | biostudies-literature
Project description:An understanding of the distribution and spatial structure of the natural vectors of zoonothic pathogens is of interest for effective disease control and prevention. Here, we investigate the range-wide population genetic structure of common pochard (Aythya ferina), a long-distance migratory duck and potential vector of highly pathogenic avian influenza. We collected several hundred samples from breeding and wintering grounds across Eurasia including some H5N1-positive individuals and generated partial sequences of the mitochondrial control region and multilocus microsatellite genotypes. Genetic differentiation among breeding populations was significant for both marker types but higher for maternally inherited mtDNA than for biparentally inherited nuclear markers. There was only weak genetic divergence between ducks sampled in Europe and East Asia, and genetic differentiation between populations was not generally associated with geographical distance. No evidence of genetic substructure was detected for ducks sampled on the European wintering grounds. Our results suggest limited breeding-site fidelity, especially in females, but extensive population admixture on the wintering grounds. The specific role of pochards as natural vectors of zoonotic pathogens and in particular H5N1 remains to be clarified but our results point to wintering grounds as potential hotspots for disease transmission.
| S-EPMC3287338 | biostudies-literature
Project description:BackgroundMolecular markers are essential to identify Echinococcus species and genotypes in areas with multiple Echinococcus species to understand their epidemiology and pathology. Tibet Autonomous Region (TAR) is one of the areas worst hit by echinococcosis. However, molecular epidemiology is still missing among echinococcosis patients in TAR. This research explored the Echinococcus species and genotypes infecting humans in TAR and the population diversity and the possible origin of G1 in TAR.MethodsCyst samples were collected in one echinococcosis-designated hospital in TAR. Echinococcus species and genotypes were identified through a maximum-likelihood approach with near-complete/complete mtDNA using IQ-TREE. Phylogenetic networks were built with PopART, and the phylogeographical diffusion pattern was identified using a Bayesian discrete phylogeographic method.ResultsUsing phylogenetic trees made with near-complete/complete mtDNA obtained from 92 cysts from TAR patients, the Echinococcus species and genotypes infecting humans in TAR were identified as Echinococcus granulosus (s.s.) G1 (81, 88.04%), accounting for the majority, followed by G6 of the E. canadensis cluster (6, 6.52%), E. granulosus (s.s.) G3 (3, 3.26%), and E. multilocularis (2, 2.17%). An expansion trend and a possible recent bottleneck event were confirmed among the G1 samples in TAR. Adding the other near-complete mtDNA of G1 samples globally from the literature, we identified the possible phylogeographic origin of the G1 samples in TAR as Turkey.ConclusionsUsing near-complete/complete mtDNA sequences of Echinococcus spp. obtained from echinococcosis patients, a variety of Echinococcus species and genotypes infecting humans throughout TAR were identified. As far as we know, this is the first comprehensive molecular investigation of Echinococcus species and genotypes infecting humans throughout TAR. We identified, for the first time to our knowledge, the possible origin of the G1 in TAR. We also enriched the long mtDNA database of Echinococcus spp. and added two complete E. multilocularis mtDNA sequences from human patients. These findings will improve our knowledge of echinococcosis, help to refine the targeted echinococcosis control measures, and serve as a valuable baseline for monitoring the Echinococcus species and genotypes mutations and trends of the Echinococcus spp. population in TAR.
| S-EPMC8898537 | biostudies-literature
Project description:The Alashan ground squirrel (Spermophilus alashanicus) is primarily distributed in the regions of Inner Mongolia and Ningxia, China. In this study, we present the first complete mitochondrial genome of S. alashanicus. The genome spans 16,464 base pairs and comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region with a marked AT bias. The overall GC content is 35.4%. Phylogenetic analyses indicate that S. alashanicus clusters are closely associated with S. dauricus. This comprehensive characterization of the S. alashanicus mitochondrial genome serves as a foundational resource for future studies on mitochondrial evolution, species identification, population genomics, and phylogenetics.
| S-EPMC10810644 | biostudies-literature