Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44472 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2698950_1.fastq.gz | Fastqsanger.gz | |||
| ERR2698950_2.fastq.gz | Fastqsanger.gz | |||
| ERR2698960_1.fastq.gz | Fastqsanger.gz | |||
| ERR2698960_2.fastq.gz | Fastqsanger.gz | |||
| ERR2698970_1.fastq.gz | Fastqsanger.gz |
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Project description:Anaplasma and Mycobacterium species are known to modify gene expression in ruminants. The objectives of this study were (a) to characterize global gene expression profiles in European red deer (Cervus elaphus) in response to Anaplasma ovis and A. ovis/Mycobacterium bovis/M. avium sub. paratuberculosis (MAP) infections, (b) to compare the expression of immune response genes between A. ovis- and A. ovis/M. bovis/MAP-infected deer, and (c) to characterize the differential expression of immune response genes identified in red deer in cattle infected with M. bovis and A. marginale. The results of this study showed that global gene differential expression in A. ovis- and A. ovis/M. bovis/MAP-infected deer results in the modification of common and pathogen-specific cellular biological processes. The differential expression of host immune response genes also showed pathogen-specific signatures and the effect of infection with multiple pathogens on red deer host immune response. These results suggested that intracellular bacteria from Anaplasma and Mycobacterium genera use similar mechanisms to infect and multiply within ruminant host cells while pathogen-specific mechanisms underline differences that could contribute to disease characterization and diagnosis in ruminants. A gene expression pre analysis was made in deers naturally infected with Anaplasma ovis and Mycobacterium complex using Affymetrix Bos taurus microarray to detect differentialy expressed genes. The immune response genes with variation in expression were analyzed by real time RT-PCR in the same samples and a bigger group of deers. A real time RT-PCR analysis was also made in Bos taurus naturally infected with Anaplasma marignale.
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Project description:RNA‐seq transcriptome analysis of peripheral blood from cattle infected with Mycobacterium bovis across an experimental time course
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Project description:Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp - 4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst=0.440) and STUB1 (Fst=0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst=0.222) and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.
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Project description:Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and B. taurus cattle Global analysis of gene expression changes in R. microplus during larval, pre-attachment and early adult stages of its life cycle feeding on Bos indicus and Bos taurus cattle were compared using gene expression microarray analysis. Among the 13 601 R. microplus transcripts from BmiGI Version 2 we identified 297 up and 17 down regulated transcripts were differentially expressed between R. microplus feeding on tick resistant cattle [Bos indicus (Brahman)] compared to R. microplus feeding on tick susceptible cattle [Bos taurus (Holstein-Friesian)]. These include genes encoding enzymes involved in primary metabolism, and genes related to stress, defence, cell wall modification, cellular signaling, receptor and cuticle. Microarrays were validated by qRT-PCR analysis of selected transcripts including the validation of three housekeeping genes. The analysis of all tick stages under survey suggested a coordinated regulation of defence proteins, proteases, and protease inhibitors to achieve successful attachment and survival of R. microplus on different host breeds particularly Bos indicus cattle. The microarray was conducted by NimbleGen Systems Inc following the method reported by Saldivar [Saldivar L et al., Insect Mol Biol 2008, 17(6):597-606]. 10 samples: 2 larva, 2 pre-attachment larva in B. indicus and 2 in B. taurus, and 2 adult ticks in B. indicus and 2 in B. taurus
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