Capra hircus
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ABSTRACT:
PROVIDER: PRJNA213437 | ENA |
REPOSITORIES: ENA
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Project description:MicroRNAs (miRNAs) are small (∼22 nucleotides) noncoding ribonucleic acids (RNAs) that regulate gene expression by binding to their complementary sequences. Recent years, a great deal of miRNAs which highly-enriched in skeletal muscle have been identified, which can influence multiple facets of muscle development and function through their regulation of key genes controlling myogenesis. However, to date no miRNAs have been reported to modulate muscle development in goat. Total RNAs from the xuhuai goats longissimus thoracis at fetal and six month old stages were used to construct small RNA libraries for Solexa SBS technology sequencing. In the small RNA profile, a total of 15,627,457 clean reads were obtained from the fetal goat library and 15,593,721 clean reads from the six month old goat library. There are 471 conserved miRNAs overlapped in both libraries, of which 343 miRNAs were differential expressed. We identified 122 novel miRNAs in the fetal caprine library and 53 novel miRNAs in the six month old-caprine library.
2015-07-19 | GSE49260 | 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. 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:The goal of this study was to compare the transcriptome profiles (RNA-seq) of fetal and six month old goat in skeletal muscle. Total RNAs from the Chinese Xuhuai goat longissimus thoracis at fetal and six month old stages were used to construct cDNA libraries for Solexa SBS technology sequencing. After remove reads with adapters, reads in which unknown bases were more than 5% and low quality reads, we obtained 27,512,850 clean reads from the fetal caprine (FC) library and 27,582,908 clean reads from the six month old caprine (SMC) library. The total basepairs were 2,476,156,500 for FC and 2,482,461,720 for SMC. The ratio of clean reads mapped to reference genome was 45.43% for FC and 33.73% for SMC. The ratio of reads mapped to reference gene was 47.77% for FC and 34.03% for SMC. To reveal the molecular events during different development stages, genes that differentially expressed between the two libraries were identified. Clean reads that matched reference genes in each library were used to evaluate the expression level of transcripts. In total, 11663 genes were differentially expressed between the two development stages. There were 5134 genes with at least a two-fold difference in expression between FC and SMC libraries (FDR, 0.001), of which 1070 genes were up-regulated, 4064 were down-regulated in the six month old caprine compared to the fetal caprine muscle tissue, and 4911 were expressed in both library. Genes with less than one fold changes between FC and SMC libraries were excluded from further analysis. The results indicated that there were significant difference between the two development phase in gene-expression. In addition, some muscle related genes such as MyoD, Myf5, Myogenin, Mrf4, myosin heavy chain 3 (MYH3), Myoglobin and DLK1 were differentially expressed.
2015-07-19 | GSE49258 | GEO
Project description:Identify differentially expressed genes between two development stages in Xuhuai goat skeletal muscle through RNA-Sequencing
| PRJNA213434 | ENA
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that regulate the post transcriptional control of several pathway intermediates, and essential for regulation in skeletal muscle of many species, such as mice, cattle, pig and so on. However, a little number of miRNAs have been reported in the muscle development of goat. In this study, the longissimus dorsi transcripts of goat at 1- and 10-month-old were analyzed for RNA-seq and miRNA-seq. The results showed that 10-month-old Longlin goat expressed 327 up- and 419 down-regulated differentially expressed genes (DEGs) compared with the 1-month-old were founded. In addition, 20 co-up-regulated and 55 co-down-regulated miRNAs involved in muscle fiber hypertrophy of goat were identified in 10-month-old Longlin and Nubian goat compared with 1-month-old. Five miRNA–mRNA pairs (chi-let-7b-3p-MIRLET7A, chi-miR193b-3p-MMP14, chi-miR-355-5p-DGAT2, novel_128-LOC102178119, novel_140-SOD3) involved in the goat skeletal muscle development were identified by miRNA–mRNA negative correlation network analysis. Our results provided an insight into the functional roles of miRNAs of goat muscle-associated miRNAs, allowing us to better understand the transformation of miRNA roles during mammalian muscle development.
2022-11-09 | GSE217092 | GEO
Project description:RNAseq of skeletal muscle from low birthweight goat and control
| PRJNA657812 | ENA
Project description:Identification of Novel and Differentially Expressed MicroRNAs in Goat Enzootic Nasal Adenocarcinoma
| PRJNA273650 | ENA
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: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.
2024-04-03 | GSE207023 | GEO