Capra hircus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA281774 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1997913_1.fastq.gz | Fastqsanger.gz | |||
| SRR1997913_2.fastq.gz | Fastqsanger.gz | |||
| SRR2001610_1.fastq.gz | Fastqsanger.gz | |||
| SRR2001610_2.fastq.gz | Fastqsanger.gz | |||
| SRR2002371_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptomic analysis provides insights into the high-altitude adaptation in domestic goats
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Project description:High-altitude adaptation is a representative example of vertebrates getting adapted to harsh and extreme environments. To investigate the miRNA expression alterations of goats that were induced by high altitude stress, we performed comparative miRNA transcriptome analysis on six hypoxia-sensitive tissues (heart, kidney, liver, lung, skeletal muscle and spleen) in two indigenous goat populations from distinct altitudes (600 m and 3000 m). We obtained the expression of 1391 mature miRNAs and identified 138 differentially expressed miRNAs between altitudes. Combined with tissue specificity analysis, we illustrated alterations of expression levels between altitudes and among tissues, which suggested the coexisting tissue-specific and tissue-conserved mechanism for hypoxia adaptation. Notably, the interplay between DE miRNA and DE target genes strongly indicated post-transcriptional regulation in HIF-1 signaling pathway, insulin signaling pathway and p53 signaling pathway, which might play a significant role in high altitude adaptation in domestic goats. These results provide insights into the complicated miRNA expression pattern and regulatory mechanism of high altitude adaptation in domestic goats.
2020-07-23 | GSE125665 | GEO
Project description:The domestic goat, Capra hircus (2n=60), is one of the most important domestic livestock species in the world. Here we report its high quality reference genome generated by combining Illumina short reads sequencing and a new automated and high throughput whole genome mapping system based on the optical mapping technology which was used to generate extremely long super-scaffolds. The N50 size of contigs, scaffolds, and super-scaffolds for the sequence assembly reported herein are 18.7 kb, 3.06 Mb, and 18.2 Mb, respectively. Almost 95% of the supper-scaffolds are anchored on chromosomes based on conserved syntenic information with cattle. The assembly is strongly supported by the RH map of goat chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Rapidly evolving genes and gene families are enriched in metabolism and immune systems, consistent with the fact that the goat is one of the most adaptable and geographically widespread livestock species. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study not only provides a high quality reference genome for an important livestock species, but also shows that the new automated optical mapping technology can be used in a de novo assembly of large genomes. Corresponding whole genome sequencing is available in NCBI BioProject PRJNA158393. We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues (Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DGE analysis. This submission represents RNA-Seq component of study.
2012-12-23 | E-GEOD-37456 | biostudies-arrayexpress
Project description:The domestic goat, Capra hircus (2n=60), is one of the most important domestic livestock species in the world. Here we report its high quality reference genome generated by combining Illumina short reads sequencing and a new automated and high throughput whole genome mapping system based on the optical mapping technology which was used to generate extremely long super-scaffolds. The N50 size of contigs, scaffolds, and super-scaffolds for the sequence assembly reported herein are 18.7 kb, 3.06 Mb, and 18.2 Mb, respectively. Almost 95% of the supper-scaffolds are anchored on chromosomes based on conserved syntenic information with cattle. The assembly is strongly supported by the RH map of goat chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Rapidly evolving genes and gene families are enriched in metabolism and immune systems, consistent with the fact that the goat is one of the most adaptable and geographically widespread livestock species. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study not only provides a high quality reference genome for an important livestock species, but also shows that the new automated optical mapping technology can be used in a de novo assembly of large genomes. We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues(Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DEG analysis. Corresponding whole genome sequencing is available in NCBI BioProject PRJNA158393.
2012-12-23 | GSE37456 | GEO
Project description:Purpose: Domestic goats distributed in a wide range of habitats and have evolved genetic adaptations to their local environmental conditions. The goal of this study s to investigate the dramatic gene expression changes of goats that are shaped by high altitude adaptation. Methods: We performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung and skeletal muscle) in three indigenous populations residing in distinct altitudes (600 m, 2,000 m and 3,000 m). Results: We identified numerous differentially expressed genes which exhibited distinct expression patterns, and nonsynonymous SNVs-containing genes which highly differentiated between the high- and low-altitude populations. Conclusions: These identified genes have known or potential roles in hypoxia response, and enriched in functional gene categories potentially responsible for high altitude adaptation, are appealing candidates for further investigation of the adaptive evolution in harsh high-altitude environment.
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Project description:Understanding molecular mechanism associated with high altitude exposure during acclimatization/adaptation/maladaptation. Data reveals specific components of the complex molecular circuitry underlying high altitude pulmonary edema. Individualized outcome prediction were constructed through expression profiling of 39400 genes in sea level sojourners who were acclimatized to high altitude and grouped as controls (n=14), high altitude natives (n=14) and individuals who developed high altitude pulmonary edema within 48-72 hours after air induction to high altitude (n=17).
2013-12-18 | E-GEOD-52209 | biostudies-arrayexpress
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