Equus ferus strain:Marwari
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA246445 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1275408_1.fastq.gz | Fastqsanger.gz | |||
| SRR1275408_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild multiple conservation efforts convened to preserve the species, including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
| S-EPMC11304947 | biostudies-literature
Project description:The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
| S-EPMC10925127 | biostudies-literature
Project description:Evaluation of the equine ocular surface microbiome before and after treatment with topical antibiotics
| PRJNA488103 | ENA
Project description:Affective states are of increasing interest in the assessment of animal welfare. This research aimed to evaluate the possible limitations in the application of a spatial judgment bias test (JBT) in horses, considering the influence of stress level, personality traits, and the possible bias due to the test structure itself. The distinction between two positions, one rewarded (Positive) and the other not (Negative), was learned by 10 horses and 4 ponies,. Then, the latency to reach three unrewarded ambiguous positions (Near Positive, Middle, Near Negative) was measured. Furthermore, the validated Equine Behavior Assessment and Research Questionnaire (E-BARQ) was employed to assess personality traits. Fecal and hair cortisol levels were measured through radioimmunoassay (RIA), and the frequency of behavioral stress indicators was recorded. Results showed that horses that had the rewarded position (Positive) on the right approached Near Negative and Middle faster than those that had Positive on the left. Certain personality traits influenced the latency to reach Middle and Near Positive, but chronic stress did not seem to affect horses' judgment bias. This preliminary study highlighted several limitations in the employment of spatial JBT for the assessment of affective state in horses and that personality traits can partially influence the cognitive process. Further research is needed to refine the use of this test in horses, considering the peculiarities both of species and of individuals.
| S-EPMC9654000 | biostudies-literature
Project description:Megafaunas worldwide have been decimated during the late Quaternary. Many extirpated species were keystone species, and their loss likely has had large effects on ecosystems. Therefore, it is increasingly considered how megafaunas can be restored. The horse (Equus ferus) is highly relevant in this context as it was once extremely widespread and, despite severe range contraction, survives in the form of domestic, feral, and originally wild horses. Further, it is a functionally important species, notably due to its ability to graze coarse, abrasive grasses. Here, we used species distribution modelling to link locations of wild-living E. ferus populations to climate to estimate climatically suitable areas for wild-living E. ferus. These models were combined with habitat information and past and present distributions of equid species to identify areas suitable for rewilding with E. ferus. Mean temperature in the coldest quarter, precipitation in the coldest quarter, and precipitation in the driest quarter emerged as the best climatic predictors. The distribution models estimated the climate to be suitable in large parts of the Americas, Eurasia, Africa, and Australia and, combined with habitat mapping, revealed large areas to be suitable for rewilding with horses within its former range, including up to 1.5 million ha within five major rewilding areas in Europe. The widespread occurrence of suitable climates and habitats within E. ferus' former range together with its important functions cause it to be a key candidate for rewilding in large parts of the world. Successful re-establishment of wild-living horse populations will require handling the complexity of human-horse relations, for example, potential conflicts with ranchers and other agriculturalists or with other conservation aims, perception as a non-native invasive species in some regions, and coverage by legislation for domestic animals.
| S-EPMC4503665 | biostudies-literature