Ontology highlight
ABSTRACT:
PROVIDER: PRJNA847156 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Secondary contact in Erebia butterflies
| PRJEB54919 | ENA
Project description:Tibetan chickens exhibit specific adaptations to high-altitude conditions compared with their lowland counterparts. To illustrate the genetic mechanisms of such adaptations in highland chickens, the genomes of four highland and four lowland chicken populations were resequenced. Our results showed that genes under positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune response, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of non-synonymous single nucleotide polymorphisms between highland and lowland populations was also analyzed by chi-square test. The results showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development, which were related to adaptations to hypoxia and intense radiation. RNA sequencing also revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Additionally, an evident admixture found in Tibetan chickens suggested a history of introgression from lowland gene pools. Overall, our data provided new insights into the unique adaptation of highland animals to extreme environments.
2016-01-26 | GSE77166 | GEO
Project description:Relative expression levels of mRNAs in chicken IEL experimentally infected with EA, EM, or ET were measured at 1 to 6 days post-infection (dpi) following primary and secondary infections. One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET. One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite. Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections. Cecum, duodenum, and jejunum were collected from the birds challenged with E. acervulina, E. maxima, and E. tenella, respectively. Uninfected control samples and one of the 3 infection group samples were labeled with different fluorescent dyes and hybridized simultaneously on the same slide using a reference design with a dye swap protocol. Thirty seven-condition experiment, Non-infected control vs. Primary or secondary EA, EM, or ET infected IEL at 1 to 6. Biological replicates: 2 replicates with dye-switching from each infection groups. Two replicates per array.
2011-08-14 | E-GEOD-31213 | biostudies-arrayexpress
Project description:Relative expression levels of mRNAs in chicken IEL experimentally infected with EA, EM, or ET were measured at 1 to 6 days post-infection (dpi) following primary and secondary infections. One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET. One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite. Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections. Cecum, duodenum, and jejunum were collected from the birds challenged with E. acervulina, E. maxima, and E. tenella, respectively. Uninfected control samples and one of the 3 infection group samples were labeled with different fluorescent dyes and hybridized simultaneously on the same slide using a reference design with a dye swap protocol.
2011-08-15 | GSE31213 | GEO
Project description:Adaptation to hypoxia is a complicated and important physiological course for organisms, but the genetic mechanism underlying the adaptation is not fully understood yet. Tibetan Chicken (T), an indigenous chicken breed in China which inhabit in high areas with an altitude above 2,900 meters. Shouguang Chicken(S) and Dwarf Recessive White Chicken (DRW), two lowland chicken breeds, were used as control groups. The heart was the first functional organ to develop during the embryonic development. Furthermore, the heart is an efficient energy converter utilizing the most appropriate fuel for a given environment. Therefore, GeneChip® Chicken Genome Array was employed to identify the differentially expressed genes in embryonic hearts of Tibetan Chicken and two lowland chicken breeds in both hypoxic and normoxic incubating environments with a genome wide profile. Keywords: stress response
2009-09-05 | GSE12675 | GEO
Project description:Campylobacter jejuni is a common cause of diarrheal disease worldwide. Human infection typically occurs through the ingestion of contaminated poultry products. We previously demonstrated that an attenuated Escherichia coli live vaccine strain expressing the C. jejuni N-glycan on its surface reduces the Campylobacter load in more than 50% of vaccinated leghorn and broiler birds to undetectable levels (responder birds), whereas the remainder of the animals were still colonized (non-responders). To understand the underlying mechanism, we conducted 3 larger scale vaccination and challenge studies using 135 broiler birds and found a similar responder/non responder effect. The submitted data were used for a genome-wide association study of the chicken responses to glycoconjugate vaccination against Campylobacter jejuni.
2021-11-01 | GSE181619 | GEO
Project description:Beak deformities (BD) of different forms have been documented in many wild birds. The phenomenon is termed as “the largest epizootic of gross abnormalities ever recorded among wild bird populations.” Frequencies of 1% to 3% of BD (crossed beaks) were found in several indigenous chickens including Silkies, Qingyuan Partridge, Huxu, and the Beijing-You (BJY) chickens (studied here). Birds with deformed beaks have poor production performance and induce higher mortality. Therefore, BD represents an economic as well as a welfare problem. Our lab have focused and performed studies on this complex trait/disease for 7 years. Therefore, we performed a single SNP, a pathways-based genome-wide association study (GWAS), and a genome-wide CNV detection with the genotype data of 48 BD (case) and 48 normal (control) birds from Affymetrix 600K HD genotyping arrays, using ROADTRIPS, SNP ratio test (SRT) and PennCNV, respectively. To the best of our knowledge, this is the first GWAS and CNV study to investigate the mutations and genomic structural variations in the deformed and normal beaks of chickens. The findings herein are worth of further functional characterization for better understanding the genetic mechanisms of BD in chickens and wild birds as well.
2017-07-21 | GSE101703 | GEO
Project description:Birds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. Here we report functional in vivo and evolutionary analyses of a Z-chromosome-linked microRNA (miR-2954) with strongly male-biased expression that was previously proposed to play a key role in sex chromosome dosage compensation1. We knocked out miR-2954 in chicken, which resulted in early embryonic lethality of homozygous knockout males, likely due to the highly specific upregulation of dosage-sensitive Z-linked target genes of miR-2954. Our evolutionary gene expression analyses further revealed that these dosage-sensitive target genes have become upregulated on the single Z in female birds during evolution. Altogether, our work unveils a scenario where evolutionary pressures on females following W gene loss led to the evolution of transcriptional upregulation of dosage-sensitive genes on the Z not only in female but also in male birds. The resulting overabundance of transcripts in males resulting from the combined activity of two dosage-sensitive Z gene copies was in turn offset by the emergence of a highly targeted miR-2954-mediated transcript degradation mechanism during avian evolution. Our findings demonstrate that birds have evolved a unique sex chromosome dosage compensation system in which a microRNA has become essential for male survival.
2024-04-17 | GSE257549 | GEO