Project description:P. multocida is the causative agent of a wide range of diseases of animals, including fowl cholera in birds. Fowl cholera isolates of P. multocida generally express a capsular polysaccharide composed of hyaluronic acid. There have been reports of spontaneous capsule loss in P. multocida fowl cholera-causing strains but the mechanism by which this occurs has not been determined. In this study, we identified three independent strains that had spontaneously lost the ability to produce capsular polysaccharide. Quantitative RT-PCR showed that these strains had significantly reduced transcription of the capsule biosynthetic genes, but DNA sequence analysis identified no mutations within the cap biosynthetic locus. However, whole genome sequencing of paired capsulated and acapsular strains identified a single nucleotide polymorphism within fis that was present only in the acapsular strain. Sequencing of fis from two independently derived spontaneous acapsular strains showed that each contained a mutation within fis. Complementation of these strains with an intact copy of fis returned normal capsule expression to all strains. Therefore, expression of a functional Fis protein is absolutely required for normal capsule expression in P. multocida.DNA microarray studies comparing one of the acapsular pairs (AL114 to AL1115) identified approximately 30 genes as down-regulated in the mutant; including pfh_B2 which encodes the filamentous hemagglutinin, a known P. multocida virulence factor and the cross protective surface antigen plpE.
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
Project description:P. multocida is the causative agent of a wide range of diseases of animals, including fowl cholera in birds. Fowl cholera isolates of P. multocida generally express a capsular polysaccharide composed of hyaluronic acid. There have been reports of spontaneous capsule loss in P. multocida fowl cholera-causing strains but the mechanism by which this occurs has not been determined. In this study, we identified three independent strains that had spontaneously lost the ability to produce capsular polysaccharide. Quantitative RT-PCR showed that these strains had significantly reduced transcription of the capsule biosynthetic genes, but DNA sequence analysis identified no mutations within the cap biosynthetic locus. However, whole genome sequencing of paired capsulated and acapsular strains identified a single nucleotide polymorphism within fis that was present only in the acapsular strain. Sequencing of fis from two independently derived spontaneous acapsular strains showed that each contained a mutation within fis. Complementation of these strains with an intact copy of fis returned normal capsule expression to all strains. Therefore, expression of a functional Fis protein is absolutely required for normal capsule expression in P. multocida.DNA microarray studies comparing one of the acapsular pairs (AL114 to AL1115) identified approximately 30 genes as down-regulated in the mutant; including pfh_B2 which encodes the filamentous hemagglutinin, a known P. multocida virulence factor and the cross protective surface antigen plpE. Biological triplicates of each strain were analysed in a single colour experimental design
Project description:The proteomic profiles of silky fowl egg yolk (SFEY) and Leghorn egg yolk (LEY) were analysed by bottom-up label-free liquid chromatography tandem-mass spectrometry (LC-MS/MS), aiming to provide a theoretical basis for understanding the proteomic and biological differences between the two yolks and further develop the nutritional and biomedical value of silky fowl eggs.
Project description:Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740. The whole blood samples were collected from Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Red Jungle Fowl (RJF), Shouguang (SG), Silkie (SK), Tibetan (TB), Wenchang (WC), and White Plymouth Rock (WR), and genomic DNA was isolated using standard phenol/chloroform extraction methods. Each test sample labeled with Cy3 was mixed with Red Jungle Fowl as reference sample labeled with Cy5. All process and analysis was performed in terms of standard NimbleGen procedure. However, due to some uncontrollable factors, none of results were obtained in three consecutive trials for CS, RIR and WL, so we had to choose a similar Agilent custom-designed 1*1.0 M array.