Dataset Information

The genome of Przewalski's horse (Equus ferus przewalskii).

ABSTRACT: 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.

SUBMITTER: Flack N

PROVIDER: S-EPMC10925127 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Publications

The genome of Przewalski's horse (<i>Equus ferus przewalskii)</i>.

Flack Nicole N Hughes Lauren L Cassens Jacob J Enriquez Maya M Gebeyehu Samrawit S Alshagawi Mohammed M Hatfield Jason J Kauffman Anna A Brown Baylor B Klaeui Caitlin C Mabrouk Islam F IF Walls Carrie C Yeater Taylor T Rivas Anne A Faulk Christopher C

bioRxiv : the preprint server for biology 20240228

The Przewalski's horse (<i>Equus ferus przewalskii</i>) 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 nucle ...[more]

PMID: 38464182

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Project description:Simple Summary Reintroduced Przewalski’s horse (RPH) has been released into the wild for 20 years, but their viability is still far away from that of sympatric wild animals. At present, RPHs cannot easily cope with climatic change, diseases and disturbance of other animals and need to be captured in the winters to be dewormed to increase their survival rate. Intestinal microbiota have been studied and are considered to be an important indicator to reflect the health status of the host. Thus, the differences in intestinal bacterial community composition and structure among RPHs, captive Przewalski’s horses, sympatric domestic horses and sympatric Mongolian wild asses were analyzed in this study, which can help to evaluate the adaptability of RPH and provide important reference information for further development of protection strategies. Abstract Intestinal microbiota play an important role in the survival of the host. However, no study to date has elucidated the adjustment of intestinal microbiota of the host during rewilding. Thus, this study aims to describe the intestinal bacterial community of reintroduced Przewalski’s horse (RPH) after being released into their original habitat for approximately 20 years in comparison with that of captive Przewalski’s horse (CPH), sympatric domestic horse (DH) and Mongolian wild ass (MWA) by sequencing the 16S rRNA gene. The results showed that the prevalent bacterial communities were different among CPHs, RPHs, DHs and MWAs at the family level. NMDS and ANOSIM analysis showed that the pattern of bacterial community composition in captive equines was distinct from that in the wild groups. It is shown that some bacteria had significant differences among different taxa (p < 0.001), such as Firmicutes, Bacteroidetes, Armatimonadetes, Clostrida, Bacteroidia, Clostridiales, Bacteroidales, Rikenellaceae and Bacteroidales_UCG-001. These bacteria were associated with the transition from in captive to in the wild (CPH and RPH), which reflected the change of environmental conditions. Meanwhile, Proteobacteria, Clostridia, Bacilli, Negativicutes, Gammaproteobacteria, Clostridiales, Bacillales, Selenomonadales, Pseudomonadales and Planococcaceae were the changed groups among RPHs, MWAs and DHs, which are related to feeding habits and diseases. Our results clearly showed the differences between intestinal microbiota in reintroduced animals and wild animals and led us to understand the survival state of reintroduced animals in the wild.

Project description:Background: Ecosystems with seasonal fluctuations in climate and food availability present physiological challenges to resident mammals and may cause "stress." The two predominant physiological responses to stressors are (1) the activation of the hypothalamic-pituitary-adrenal axis and (2) the modulation of the autonomic nervous system. To date, the primary indicator for "stress" in wildlife- and zoo animal research are glucocorticoid levels. By measuring the autonomic regulation of cardiac activity, particularly the vagal tone, heart rate variability (HRV) is presently emerging as a suitable indicator of "stress" in farm- and domestic animal research. Objective: The aim of this study was to use HRV, a novel method in wildlife research, to assess seasonal patterns of "stress" in a group of free-ranging Przewalski's horses (Equus ferus przewalskii). Methods: Six pregnant Przewalski's horses from one harem within the Hortobágy National Park in Hungary were subjected to the study. We used a dedicated telemetry system consisting of a subcutaneously implanted transmitter and a receiver and storage unit in a collar to record HRV, heart rate (HR), subcutaneous body temperature, and activity throughout a one-year study period-climate data was also collected. We defined "stress" as a decrease in parasympathetic nervous system tone and calculated RMSSD (root mean square of successive differences) as a measure of HRV. Linear mixed effects models with random intercept per individual were used for statistical analysis. Results: HRV and HR varied considerably throughout the year. Similar to temperate ruminants and hibernating mammals, Przewalski's horses experienced lower HR and HRV during winter, when resources are limited indicating decreased metabolic rates coupled with "stress." In spring, we observed a drop of HRV along with a peak in HR indicating an increase of allostatic load that is most likely associated with increased energy demands during pregnancy and/or seasonal routines such as the adjustment of the gastrointestinal system to better quality diet. Conclusion: Measuring telemetric HRV is a proven method to study undisturbed reactions of wild animals to their changing environment over the long term. Przewalski's horses experience a loss of complexity in cardiovascular dynamics over the winter and particularly during spring, indicating seasonal "stress."

Dataset Information

The genome of Przewalski's horse (Equus ferus przewalskii).

Publications

The genome of Przewalski's horse (<i>Equus ferus przewalskii)</i>.

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