Complete Genome Sequence of a Virulent Newcastle Disease Virus Strain Isolated from a Clinically Healthy Duck (Anas platyrhynchos domesticus) in Pakistan.
Ontology highlight
ABSTRACT:
SUBMITTER: Wajid A
PROVIDER: S-EPMC4966463 | biostudies-literature | 2016 Jul
REPOSITORIES: biostudies-literature
Publications
Complete Genome Sequence of a Virulent Newcastle Disease Virus Strain Isolated from a Clinically Healthy Duck (Anas platyrhynchos domesticus) in Pakistan.
Wajid Abdul A Rehmani Shafqat F SF Wasim Muhammad M Basharat Asma A Bibi Tasra T Arif Saima S Dimitrov Kiril M KM Afonso Claudio L CL
Genome announcements 20160728 4
Here, we report the complete genome sequence of a virulent Newcastle disease virus (vNDV) strain, duck/Pakistan/Lahore/AW-123/2015, isolated from apparently healthy laying ducks (Anas platyrhynchos domesticus) from the province of Punjab, Pakistan. The virus has a genome length of 15,192 nucleotides and is classified as member of subgenotype VIIi, class II. ...[more]
Similar Datasets
Project description:BackgroundNewcastle disease is very pathogenic in chickens, whereas in ducks, the disease does not show any clinical symptoms.AimsTo compare the clinical symptoms features, pathological lesions, viral distribution, and apoptosis response caused by the Newcastle disease virus (NDV) in domestic chicken and Alabio duck.MethodsForty domestic chickens and 40 Alabio ducks were separated into four groups: domestic chicken and Alabio duck treatment groups, where each was infected by NDV velogenic ducks/Aceh Besar_IND/2013/eoAC080721 in 106ELD50 dosage. The domestic chicken and Alabio duck control groups were each inoculated with Phosphate Buffer Saline. The infection route was intraorbital, 0.1 ml in volume. Symptoms were observed from day 1 until day 7 post-infection (PI). Necropsy was performed on days 1, 2, 3, 5, and 7 PI for organ collection.ResultsSymptoms observed were disorders in the respiratory, gastrointestinal, and nervous systems, followed by 100% mortality in domestic chickens. In Alabio ducks, there were only depression and slight lethargy. The lesion in domestic chicken day 1 appeared by the lungs, thymus, Fabricius bursa, spleen, and kidney. On day 3 PI, lesions were also found in the heart, proventriculus, duodenum, and cecal tonsil. On days 5 and 7 PI, the trachea and brain lesions were found. In Alabio ducks, lesions were found in the lungs, thymus, spleen, and proventriculus on day 1. Afterward, on day 3, light lesions were found in the heart. On day 5, lesions were found in the trachea and brain; finally, on day 7, light lesions were only found in the thymus, spleen, and brain. Immunopositive reaction NDV in domestic chicken was highest in the proventriculus, duodenum, cecal tonsil, and lymphoreticular organs. In the Alabio duck, it was highest in the duodenum and cecal tonsil. The caspase-3 percentage in domestic chicken increased on day 3 PI; in Alabio ducks, on day 2 PI.ConclusionClinical symptoms and pathological lesions were faster and more severe in domestic chickens. The immunopositive reaction NDV in domestic chicken continued to increase, while in Alabio ducks, it decreased until the last observation day. Apoptosis percentage increased earlier in the Alabio duck than in domestic chicken.
| S-EPMC10219819 | biostudies-literature
Project description:Myoblasts isolated from duck embryonic muscle were purified and in vitro cultured. External characteristics were observed by using the immunofluorescence technique, and growth curve of duck embryonic myoblasts was established after measuring with the MTT method. Moreover, mRNA expression of three marker genes, the Desmin, the muscle creatine kinase (Mck) and the troponin C (Tnnc), which could reflect the development status of myofibers, were detected each 24 h for cultured cells by using the qPCR technique. Results showed that the in vitro cultured duck myoblasts went through a series of developmental stages, including the proliferation of myoblasts, the differentiation of multi-nuclei myotubes, and the formation of myofiber. The cultured duck embryonic myoblasts entered into a logarithmic stage approximately on the fourth day after seeding. Accompanying with its progressive growth before entering into the logarithmic phase, the myoblasts also showed some differentiation phenomena, reflected by a low expression level of Desmin and high expression level of the Mck and Tnnc genes. During the rapid growth of the logarithmic phase, there was a high expression of the Desmin gene, and a low expression level of the Mck gene and the Tnnc gene in the cultured myoblasts. The expression profiles of the three marker genes for muscle development could be used for distinguishing the different developmental stages of in vitro cultured myoblasts at the molecular level, which would be more accurate and more feasible than observing the external characteristics of the cultured cells.
| S-EPMC3140835 | biostudies-literature
Project description:In the present study, we isolated preadipocytes from the adipose tissue of Peking duck and subsequently cultured them in vitro. Cell counting kit-8 assay was employed to establish the growth curve of duck primary preadipocytes. Meanwhile, after the cells reaching full confluency, they were induced to differentiate into mature adipocytes by the addition of a cocktail containing dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and oleic acid for 8 days. Successful differentiation was demonstrated by the development of lipid droplets and the expression of key marker genes including peroxisome proliferator-activated receptor-γ (PPARγ), CCAAT/enhancer binding protein-α (CEBP/α) and adipocyte fatty acid-binding protein (FABP4). Our results showed that duck primary preadipocytes began to adhere 12 h after seeding as short spindle shapes or litter triangles, which grew quickly 3 days post attachment and maintained stable after day 7. After 8 days the preadipocytes were induced to differentiate into mature adipocytes, which were stained red by oil red O. Additionally, it showed that during preadipocyte differentiation PPARγ mRNA was highly expressed at day 3, while CEBP/α and FABP4 mRNA peaked at day 5 and 8, respectively. These results indicate that we have successfully isolated and cultured Peking duck preadipocytes and successfully induced them to differentiate into mature adipocytes. This work could lay a foundation for further research into waterfowl adipogenesis.
| S-EPMC4545434 | biostudies-literature
Project description:The interferon-induced proteins with tetratricopeptide repeats (IFITs) protein family mediates antiviral effects by inhibiting translation initiation, cell proliferation, and migration in the interferon (IFN) dependent innate immune system. Several members of this family, including IFIT1, IFIT2, IFIT3 and IFIT5, have been heavily studied in mammals. Avian species contain only one family member, IFIT5, and little is known about the role of this protein in birds. In this study, duck IFIT5 (duIFIT5) full-length mRNA was cloned by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of the cDNA ends (RACE). Based on the sequence obtained, we performed a series of bioinformatics analyses, and found that duIFIT5 was most similar to homologs in other avian species. Also, duIFIT5 contained eight conserved TPR motifs and two conserved multi-domains (TPR_11 and TPR_12). Finally, we used duck hepatitis virus type 1 (DHV-1) and polyriboinosinicpolyribocytidylic acid (poly (I:C)) as a pathogen or a pathogen-associated molecular pattern induction to infect three-day-old domestic ducklings. The liver and spleen were collected to detect the change in duIFIT5 transcript level upon infection by quantitative real-time PCR (qRT-PCR). DuIFIT5 expression rapidly increased after DHV-1 infection and maintained a high level, while the transcripts of duIFIT5 peaked at 8h after poly (I:C) infection and then returned to normal. Taken together, these results provide a greater understanding of avian IFIT5.
| S-EPMC4376821 | biostudies-literature
Project description:SERPINA1 is a member of serine protease inhibitors and is increasingly considered to be a regulator of innate immunity in human and animals. However, the expression and function of SERPINA1 gene in immune defense against viral infection remain unknown in ducks. The full-length du SERPINA1 cDNA sequence was obtained using reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). It contained 1457 nucleotide, including 47-bp 5' UTR, 135-bp 3' UTR, and 1275-bp open reading frame (ORF), and encodes a 424-amino acid protein. Then, the tissue expression profile of du SERPINA1 gene was determined. Real-time quantitative polymerase chain reaction (real-time qPCR) analysis revealed that du SERPINA1 mRNA is ubiquitous in various tissues, but higher expression levels were observed in lung and liver tissues. In addition, the expression pattern was investigated when the ducklings were challenged with duck hepatitis virus 1(DHV-1) and polyriboinosinic polyribocytidylic acid (poly I:C). After DHV-1 injection or poly I:C treatment, du SERPINA1 mRNA was up-regulated in the liver and kidney tissues. However, the peak time in two tissues was not consistent. In kidney, the expression lever of SERPINA1 increased immediately after the treatment while in liver tissue it kept steady until 12 h post-infection. Our results indicate that SERPINA1 has an active role in the antiviral response, and thus improve our understanding of the role of this protein.
| S-EPMC6444226 | biostudies-literature
Project description:A genetic linkage map for the duck (Anas platyrhynchos) was developed within a cross between two extreme Peking duck lines by linkage analysis of 155 polymorphic microsatellite markers, including 84 novel markers reported in this study. A total of 115 microsatellite markers were placed into 19 linkage groups. The sex-averaged map spans 1353.3 cM, with an average interval distance of 15.04 cM. The male map covers 1415 cM, whereas the female map covers only 1387.6 cM. All of the flanking sequences of the 155 polymorphic loci--44 monomorphic loci and a further 41 reported microsatellite loci for duck--were blasted against the chicken genomic sequence, and corresponding orthologs were found for 49. To integrate the genetic and cytogenetic map of the duck genome, 28 BAC clones were screened from a chicken BAC library using the specific PCR primers and localized to duck chromosomes by FISH, respectively. Of 28 BAC clones, 24 were detected definitely on duck chromosomes. Thus, 11 of 19 linkage groups were localized to 10 duck chromosomes. This genetic and cytogenetic map will be helpful for the mapping QTL in duck for breeding applications and for conducting genomic comparisons between chicken and duck.
| S-EPMC1461431 | biostudies-literature
Project description:We report here the complete genome sequence of a Newcastle disease virus isolate, NDV/Yakutiya/mallard/852/2011, isolated from a mallard in Russia. On the basis of phylogenetic analysis, this strain was clustered into class II genotype Ib.
| S-EPMC4669403 | biostudies-literature
Project description:Duck (Anas platyrhynchos), one of the most economically important waterfowl, is an ideal model for studying the immune protection mechanism of birds. An incomplete duck reference genome and very limited availability of full-length cDNAs has hindered the identification of alternatively spliced transcripts and slowed down many basic studies in ducks. We applied PacBio Iso-Seq technologies to multiple tissues from duck for use in transcriptome sequencing. We obtained 199,993 full-length transcripts and comprehensively annotated these transcripts. 23,755 lncRNAs were predicted from all identified transcripts and 35,031 alternative splicing events, which divided into 5 models, were accurately predicted from 3,346 genes. Our data constitute a large increase in the known number of both lncRNA, and alternatively spliced transcripts of duck and plays an important role in improving current genome annotation. In addition, the data will be extremely useful for functional studies in other birds.
| S-EPMC6872741 | biostudies-literature
Project description:Background: Skeletal muscle growth and development is highly orchestrated in gene expressions. Understanding the location-specific and breed-specific genes and pathways are agriculturally important on meat products and meat quality. In the present study, RNA-Seq was performed to elucidate the difference of muscle deposition between locations and breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected for pectoral muscle (PM) and leg muscle (LM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared location-specific genes between PM and LM, while Experiment 2 compared the two breeds (H and P) at the same development stage (embryonic 15 days). Results: Almost 13 million clean reads was generated using Illumina technology on each library, and more than 70% reads mapped to Anas platyrhynchos breed Peking duck genome. We identified 246, 258, 20 and 54 differentially expressed genes (DEGs) (log2.fold-change >0.5, and P-value <0.05) for H-PM vs H-LM, P-PM vs P-LM, H-LM vs P-LM and H-PM vs P-PM library, separately. A total of 168 genes were differentially expressed by over locations in experiment 1, while only 8 genes were differentially expressed by over breeds in experiment 2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DGEs. In experiment 1, DEGs mainly involved in Focal adhesion, PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In experiment 2, DEGs only associated with ribosome signal pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was employed to confirm 15 differentially expressed genes detected by RNA-Seq. Conclusions: Comparative transcript analysis of leg muscle and pectoral muscle of two duck breeds not only improves our understanding of those location-specific and breed-specific genes and pathways, but also provides some candidate molecular targets for increase muscle products and meat quality by genetic control. Conclusions: Our study represents the first detailed analysis of duck breed muscle transcriptomes generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2015-12-30 | GSE65628 | GEO
Project description:Short tandem repeats (STRs) are usually associated with genetic diseases and gene regulatory functions, and are also important genetic markers for analysis of evolutionary, genetic diversity and forensic. However, for the majority of STRs in the duck genome, their population genetic properties and functional impacts remain poorly defined. Recent advent of next generation sequencing (NGS) has offered an opportunity for profiling large numbers of polymorphic STRs. Here, we reported a population-scale analysis of STR variation using genome resequencing in mallard and Pekin duck. Our analysis provided the first genome-wide duck STR reference including 198,022 STR loci with motif size of 2-6 base pairs. We observed a relatively uneven distribution of STRs in different genomic regions, which indicates that the occurrence of STRs in duck genome is not random, but undergoes a directional selection pressure. Using genome resequencing data of 23 mallard and 26 Pekin ducks, we successfully identified 89,891 polymorphic STR loci. Intensive analysis of this dataset suggested that shorter repeat motif, longer reference tract length, higher purity, and residing outside of a coding region are all associated with an increase in STR variability. STR genotypes were utilized for population genetic analysis, and the results showed that population structure and divergence patterns among population groups can be efficiently captured. In addition, comparison between Pekin duck and mallard identified 3,122 STRs with extremely divergent allele frequency, which overlapped with a set of genes related to nervous system, energy metabolism and behavior. The evolutionary analysis revealed that the genes containing divergent STRs may play important roles in phenotypic changes during duck domestication. The variation analysis of STRs in population scale provides valuable resource for future study of genetic diversity and genome evolution in duck.
| S-EPMC6218588 | biostudies-literature