Emissaries of the past?: Whole genome assessment of the genetic diversity and origin of Danube’s Delta horses
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB89292 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.
| S-EPMC6070244 | biostudies-literature
Project description:Custom exon aCGH analysis of copy number across the genomes of 16 horse breeds
2011-10-08 | GSE32702 | GEO
Project description:Custom exon aCGH analysis of copy number across the genomes of 16 horse breeds Two-condition experiment, All breed samples were compared to a single Thoroughbred reference, Reference was then compared to Twilight (DNA from horse used for reference genome assembly)
2011-10-07 | E-GEOD-32702 | biostudies-arrayexpress
Project description:Twenty-one pheromone-induced genes were selected from the literature (Zhao, Daniels et al. 2005 was the major source) as the reference set for assessing the pheromone response of CAI4 (Wild-type), cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains.Our aim was to check whether or not these 21 pheromone-induced genes are up-regulated in response to pheromone in each mutant strain.
2019-01-26 | GSE125636 | GEO
Project description:We sequenced the whole mRNA of six thoroughbred horse (Equus caballus) blood and muscle tissues before and after exercising, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising. whole mRNA sequencing profiles of six thoroughbred horse (Equus caballus) blood and muscle tissues before and after exercising
2013-05-01 | E-GEOD-37870 | biostudies-arrayexpress
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. cricoarytenoideus dorsalis muscle), liver, lung, mammary gland, mitral valve of the heart, skeletal muscle (gluteal muscle and longissimus muscle), occipital cortex, ovary, parietal cortex, pituitary, sacrocaudalis dorsalis muscle, skin, spinal cord (C1 and T8), spleen, suspensory ligament, temporal cortex, tendon (deep digital flexor tendon and superficial digital flexor tendon), uterus.
2021-11-25 | GSE174767 | GEO
Project description:BMA64 rrp6 delta::HIS3 vs BMA64 WT (Mat a), grown at 30°C to OD 0.6 in YPD. BMA64 rrp6 delta::URA3, trf4 delta::KAN vs BMA64 WT, grown at 30°C to OD<0.6 in YPD. Keywords: other
2005-04-28 | GSE2579 | GEO
Project description:The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
| S-EPMC5068837 | biostudies-literature
Project description:We sequenced the whole mRNA of six thoroughbred horse (Equus caballus) blood and muscle tissues before and after exercising, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.
2013-05-01 | GSE37870 | GEO
Project description:Proteomic comparsion of Bacteroides thetaiotaomicron OMV, TM and WC of delta BT4720, delta BT_4721, delta BT_4720_4721 and WT
2024-02-08 | PXD043360 | Pride