Capra hircus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA596079 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12052364.fastq.gz | Fastqsanger.gz | |||
| SRR12052365.fastq.gz | Fastqsanger.gz | |||
| SRR12052366.fastq.gz | Fastqsanger.gz | |||
| SRR12052367.fastq.gz | Fastqsanger.gz | |||
| SRR12052368.fastq.gz | Fastqsanger.gz |
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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: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:Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. Results We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals. Conclusions We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.
2010-11-09 | GSE24436 | GEO
Project description:The present study, for the first time, compared the transcriptomes of ovaries from the prolific Jintang black goat and the non-prolific Tibetan goat during follicular phase using the Illumina RNA-Seq method. The study provides insight into the transcriptional regulation in the ovaries of two distinct breeds of goats that might serve as a key resource for understanding goat fecundity.
2017-11-22 | GSE87878 | GEO
Project description:Capra hircus Rumen Epithelial Transcriptome, Small RNA seq and Single nucleus RNA seq
| PRJNA1165347 | ENA
Project description:The study confirmed a batch of goat skin and hair follicles miRNA, by high-throughput sequencing methods.316 sequences miRNAs were obtained by the means of analysis and we confirmed the authenticity of 68 known miRNAs and discovered 248 novel miRNAs, as well as 22 miRNAs that haven’t been reported before. Through the miRNAs family analysis, we found the co-expressed miRNAs in goat and sheep located in the same region of chromosome, which may play an essential role in skin and follicle development. In addition, the prediction of novel target miRNAs followed by the analysis of target gene pathways indicated that MAPK pathway may have an important effect to the fast growth of skin follicle cell.
2012-02-25 | GSE36052 | GEO
Project description:Molecular mechanisms of follicular atresia and prolificacy of mammal remain unclear. We surveyed the single-cell transcriptomic landscape of ovaries from single and prolificacy goat and identified seven ovarian cell types with distinct gene-expression, transcriptional factor networks and reciprocal interactions signatures. In-depth dissection of gene-expression dynamics of granulosa cells (GCs) that displayed development stage-specific expression patterns and specific gene signatures were identified that may reflect developmental competency and ovarian reserve. what’s more, we revealed the origin of theca cells. Further analysis of cell-type-specific prolificacy-associated transcriptional changes uncovered apoptosis, anabolism and response to hormone stimulation as are crucial factor in dominant follicle development and ovulation. Additionally, differentially expressed genes (DEGs) of SERPINE2 can interact with CYP19A1 to promote cell proliferation, inhibit apoptosis and promoting the anabolism were observed in mouse granulosa cells. Thus, our work provides a comprehensive understanding of the cell-type-specific mechanisms underlying goat ovarian prolificacy at single-cell resolution, provides key insights into offers important clues for improving follicle recruitment in vivo and revealing new diagnostic biomarkers and potential therapeutic targets for ovulation disorder.
2024-06-29 | GSE206398 | GEO
Project description:We report the application of Solexa high-throuthput sequencing technology for miRNA differential expression profiles. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to Ovis aries genome. The results were validated by qRT-PCR. Our study represents the first detailed analysis of miRNA expression profiles in goat mammary gland tissues, with biologic replicates generated by RNA-seq technology. miRNA expression profiles of goat mammary gland tissues between peak lactation and late lactation were generated by Illumina/Solexa sequencing
2013-01-01 | E-GEOD-39484 | biostudies-arrayexpress