Pink-headed duck WGS data
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB97953 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We deep sequenced and analyzed miRNAs using deep RNA sequencing (RNA-seq) in transported and control duck's duodenum sample of Jingjiang duck. We analyzed the miRNA data with 9467248 reads and 9808143 million reads, obtained 9338224 and 9677777 clean reads in transported and control duck's by high-throughput sequencing, respectively. we respectively gained 4636135 and 4759049 miRNAs sequences in two groups by filtering the known non-miRNA reads, such as rRNA, tRNA, snRNA, and snoRNA by screening against ncRNA deposited in the GenBank and Rfam databases. These findings provided insights into the expression profiles of miRNAs in duck duodenum, and deepened our understanding of miRNAs in transportation injury of duck.
2018-12-31 | GSE104798 | GEO
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Project description:The first molecular phylogenetic hypothesis for the possibly extinct pink-headed duck Rhodonessa caryophyllacea unambiguously shows that it belongs to the pochard radiation that also includes the genera Aythya and Netta. It is the sister to all modern-day pochards and belongs to a lineage that branched off from the others more than 2.8 million years ago. Rhodonessa caryophyllacea is believed to never have been common in modern time and we show this has probably been the situation for as long as 100,000 years. Our results suggest that their effective population size varied between 15,000 and 25,000 individuals during the last 150,000 years of the Pleistocene. The reasons behind this are largely unknown as very little is known about the life-history and biology of this species. Presumably it is due to factors related to feeding or to breeding, but we may never know this for sure.
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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.
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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.
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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.
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