Capra hircus breed:San Clemente
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ABSTRACT:
PROVIDER: PRJNA613782 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Capra hircus breed:San Clemente Genome sequencing and assembly
| PRJNA290100 | ENA
Project description:Capra hircus breed:Capra hircus Raw sequence reads
| PRJNA786385 | ENA
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:Expressional alterations and post translational modifications (PTM) of type II collagen can be major cause behind osteo and rheumatoid arthritis. PTM of type II collagen α1 chain (COL2A1) such as hydroxylation of proline (P), lysine and glycosylation of hydroxylysine can act as epitopes resulting COL2A1 as autoantigen in cartilage tissues. Previous study stated proline hydroxylation (Hyp) as an important PTM in type II collagen leading to dysfunctional collagen extracellular matrix assembly in vivo. Here we report for the first time peptide mass fingerprinting (PMF) identification and tandem mass spectrometry based mapping of Hyp PTM in COL2A1 from Capra hircus (C. hircus) using Mascot database. As mascot database does not contain C. hircus COL2A1 sequence information, our identification is based on the homologous COL2A1 from Bos taurus and Homo sapience (above 98 % identity). Findings include identification of new triplet Gly-F-Hyp in C. hircus COL2A1 and well known Gly-X-Y triplet with Hyp present in the X position, instead of Y position. PMF data contains lager number of Hyp in COL2A1 from C. hircus consistent with other collagen sequences. This study suggests positional alteration of Hyp/P in Gly-X-Y triplet may be used for molecular identification and characterization of type II collagen from other sources.
2019-05-06 | PXD012928 | Pride
Project description:Expressional alterations and post translational modifications (PTM) of type II collagen can be major cause behind osteo and rheumatoid arthritis. PTM of type II collagen α1 chain (COL2A1) such as hydroxylation of proline (P), lysine and glycosylation of hydroxylysine can act as epitopes resulting COL2A1 as autoantigen in cartilage tissues. Previous study stated proline hydroxylation (Hyp) as an important PTM in type II collagen leading to dysfunctional collagen extracellular matrix assembly in vivo. Here we report for the first time peptide mass fingerprinting (PMF) identification and tandem mass spectrometry based mapping of Hyp PTM in COL2A1 from Capra hircus (C. hircus) using Mascot database. As mascot database does not contain C. hircus COL2A1 sequence information, our identification is based on the homologous COL2A1 from Bos taurus and Homo sapience (above 98 % identity). Findings include identification of new triplet Gly-F-Hyp in C. hircus COL2A1 and well known Gly-X-Y triplet with Hyp present in the X position, instead of Y position. PMF data contains lager number of Hyp in COL2A1 from C. hircus consistent with other collagen sequences. This study suggests positional alteration of Hyp/P in Gly-X-Y triplet may be used for molecular identification and characterization of type II collagen from other sources.
2019-05-06 | PXD012911 | Pride
Project description:Capra hircus breed:goat Genome sequencing and assembly
| PRJNA796784 | ENA
Project description:Capra hircus breed:goat Genome sequencing and assembly
| PRJNA454745 | ENA