Genome and transcriptome of the duck
Ontology highlight
ABSTRACT:
ORGANISM(S): Anas platyrhynchos
PROVIDER: GSE22967 | GEO | 2013/04/01
REPOSITORIES: GEO
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Project description:The reads of duck transcripome was mapped to the duck genome and help to identify the UTR regions of predicted genes. The expression level difference between the tissue spleen and liver will help us to detect the immune-related and fatty acid metabolism related genes. Duck transcriptome was sequenced to improve the gene annotation quality, and to detect the differently expressed genes in liver and spleen tissues.
2013-04-01 | E-GEOD-22967 | biostudies-arrayexpress
Project description:Purpose:To understand the transcriptome regulator of duck spleen infected with duck enteritis virus (DEV).Methods:50-day-old ducks were inoculated with 100 titer (The TCID50 of DEV was 10-9/0.1mL) and 10-2 titer two different viral titer of DEV in leg muscle for different durations (66 h, 90 h and 114 h) and seronegative control (0 h) were analyzed using next-generation RNA sequencing.Furthermore, the data were validated using quantitative real-time PCR.Results:There were 534, 685 and 580 genes differentially expressed in 100 titer, moreover, 511, 485 and 531 differentially expressed genes (DEGs) were obtained from 10-2 titer for 66 h, 90 h and 114 h, respectively. These genes were mainly involved in functional categories including immune response, extracellular space, heparin binding, oxygen transport, extracellular region, cellular response to interleukin-4, MHC class II protein complex, antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, and pathways such as ribosome, ECM-receptor interaction, cell adhesion molecules, JAk-STAT signaling pathway, PPAR signaling pathway, neuroactive ligand-receptor interaction, phagosome.Conclusions: Different titers of DEV infection can stimulate different biological processes and signaling pathways in the spleen, and regulated the complex biological processes, metabolic and signaling pathways in the process of DEV infection.This transcriptome analysis of duck spleen infected with DEV in different time points is reported for the first time, it laid the foundation for further understanding of interactions between DEV and duck spleen tissue, molecular mechanisms of duck defend against DEV infection, and screening key functional genes.
2020-06-27 | GSE100524 | GEO
Project description:Duck reovirus (DRV), a member of the genus Orthoreovirus in the family Reoviridae, was first isolated from Muscovy ducks. The disease associated with DRV causes great economic losses to the duck industry. However, the responses of duck (Cairna moschata) to the classical/novel DRV (C/NDRV) infections are largely unknown. To reveal the relationship of pathogenesis and immune response, the proteomes of duck spleen cells under the control and C/NDRV infections were compared. In total, 5986 proteins were identified, of which 5389 proteins were quantified. The different expressed proteins (DEPs) under the C/NDRV infections showed displayed various biological functions and diverse subcellular localizations. The proteins related to the serine protease system were siginificantly changed, suggesting that the activated serine protease system may play an important role under the C/NDRV infections. Furthermore, the differences in the responses to the C/NRDV infections between the duck liver and spleen cells were compared. Only a small number of common DEPs were identified in both liver and spleen cells, suggesting diversified pattern involved in the responses to the C/NRDV infections. However, the changes in the proteins involved in the serine protease systems were similar in both liver and spleen cells. Our data may give a comprehensive resource for investigating the responses to C/NDRV infections in ducks.
2020-08-24 | PXD009703 | Pride
Project description:The novel duck reovirus (NDRV) can cause hemorrhage and necrosis on the spleen of Pekin ducks, this disease has resulted in great economic losses to the duck industry. However, the molecular pathogenesis of NDRV remains poorly understood. In the current study, the quantitative proteomic analysis of NDRV-infected duck embryo fibroblasts was performed to explore the cellular protein changes in response to viral infection through iTRAQ coupled with the LC–MS/MS method. A total of 6,137 proteins were obtained in cell samples at 24 hours post infection. Of these, 179 differentially expressed proteins (DEPs) were identified (cutoff set to 1.5-fold change), including 89 upregulated and 90 downregulated proteins. Bioinformatic analysis showed that DEPs can be divided into the cellular component, molecular function, and biological process, they were mainly involved in the signal transduction, infectious diseases, cell growth and death, and the immune system. The subcellular localization of most proteins was cytoplasm. Importantly, the expression of signal transducer and activator of transcription 1 (STAT1) and various interferon-stimulated genes (ISGs) were upregulated after NDRV infection. The mRNA transcripts of some ISGs were consistent with proteomic data, showing an increased trend. Results of our study suggested that NDRV infection can elicit the strong expression changes of cellular proteins, and activate the expression of ISGs from the point of quantitative proteomic analysis. The study provides a new insight into the understanding of NDRV pathogenesis.
2021-09-07 | PXD020171 | Pride
Project description:Domestic duck and distantly related Anas species Genome sequencing and assembly
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Project description:Duck reovirus (DRV) is a fatal member of the genus Orthoreovirus in the family Reoviridae. The disease caused by DRV leads to huge economic losses to the duck industry. Post-translational modification is an efficient strategy to enhance the immune responses to virus infection. However, the roles of protein phosphorylation in the responses of ducklings to Classic/Novel DRV (C/NDRV) infections are largely unknown. Using a high-resolution LC-MS/MS integrated to highly sensitive immune-affinity antibody method, phosphoproteomes of Cairna moschata spleen tissues under the C/NDRV infections were analyzed, producing a total of 8,504 phosphorylation sites on 2,853 proteins. After normalization with proteomic data, 392 sites on 288 proteins and 484 sites on 342 proteins were significantly changed under the C/NDRV infections, respectively. To characterize the differentially phosphorylated proteins (DPPs), a systematic bioinformatics analyses including Gene Ontology annotation, domain annotation, subcellular localization, and Kyoto Encyclopedia of Genes and Genomes pathway annotation were performed. Two important serine protease system-related proteins, coagulation factor X and fibrinogen α-chain, were identified as phosphorylated proteins, suggesting an involvement of blood coagulation under the C/NDRV infections. Furthermore, 16 proteins involving the intracellular signaling pathways of pattern-recognition receptors were identified as phosphorylated proteins. Changes in the phosphorylation levels of MyD88, NF-κB, RIP1, MDA5 and IRF7 suggested a crucial role of protein phosphorylation in host immune responses of C. moschata. Our study provides new insights into the responses of ducklings to the C/NDRV infections at PTM level.
2021-09-09 | PXD016423 | Pride
Project description:We deep sequenced and analyzed miRNAs using deep RNA sequencing (RNA-seq) in cage rearing and traditional breeding duck's duodenum sample of Nonghu NO.2 duck. 21 differentially expressed miRNA were identified in the duodenum. 6 miRNAs were upregulated and 15 were downregulated in the cage rearing duck's duodenum of the Nonghu NO.2 duck compared to their expression in the control group. These findings provided insights into the expression profiles of miRNAs in duck duodenum, and deepened our understanding of miRNAs in oxidative injury of duck.
2023-07-23 | GSE237634 | GEO
Project description:Hatchability is one of the important reproductive traits of poulty, however, molecular biological study related to hatchability of poultry is very limited. The magnum is where the egg white components are produced. During embryo development, egg white secreted by the magnum is gradually transferred into the amniotic fluid, and albumen finally migrates to the embryo. Egg white proteins are composed of ovalbumin, conalbumin, lysozyme, ovomucoid, riboflavin binding protein (RfBP), and other less abundant proteins. Mutation of ovalbumin and RfBP genes increases the mortality of embryos; therefore, egg white might be closely related to poultry hatchability. Tsaiya duck (Anas platyrhynchos) is the major egg-laying duck in Taiwan. In this study, gene expression profiling by cDNA microarray chip technology was performed using mRNA prepared from the magnum epithelium of Tsaiya ducks, and a number of differentially expressed transcripts were found. Keywords = Tsaiya duck (Anas platyrhynchos), magnum, hachability, cDNA microarray, transcriptional profiling.
2010-11-16 | GSE23100 | GEO
Project description:Duck Tembusu virus (DTMUV) is a newly emerging pathogenic flavivirus that has caused huge economic losses to the duck industry in China since 2010. Moreover, DTMUV can also infect geese, chickens, house sparrows and replicate in in the brain, spleen, liver and kidneys of BALB/c mice, which poses public health concerns. So developing vaccines to combat DTMUV becomes urgent. Baby hamster kidney cell line (BHK-21) is usually employed to produce veterinary vaccine and DTMUV as well as other flaviviruses can be propagated in BHK-21 cells. However, information about mammalian host cell responses to DTMUV infection is limited. In this study, LC–MS/MS coupled to iTRAQ labeling was used to quantitatively identify differentially expressed cellular proteins in DTMUV-infected BHK-21 cells. We identified 192 differentially expressed cellular proteins including 11 upregulated proteins and 8 downregulated at 24 hpostinfection; 25 upregulated proteins and 151 downregulated at 48 h postinfection. Some of these proteins were involved in viral infection.
2017-05-23 | PXD005731 | Pride
Project description:The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to growth of duck skeletal muscle. RNA-sequencing technology was used to com-pare the transcriptome of duck breast muscles in an F2 population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be ex-pressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified be-tween the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the FABP3 and MYL4 involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks, and provided a theoretical basis for improving duck production and breeding of ducks.
2021-10-24 | GSE185612 | GEO