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Scientific reports2025; 15(1); 6803; doi: 10.1038/s41598-025-91564-1

Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses.

Abstract: Mitochondria are semi-autonomous organelles that play a crucial role in the energy budget of animal cells and are closely related to the locomotor abilities of animals. Equidae is renowned for including two domesticated species with distinct purposes: the endurance-oriented donkey and the power-driven horse, making it an ideal system for studying the relationship between mitochondria and locomotor abilities. In this study, to cover the genetic diversity of donkeys, we sequenced and assembled six new mitochondrial genomes from China. Meanwhile, we downloaded the published mitochondrial genomes of all species within Equus and conducted a comprehensive pan-mitochondrial genome analysis. We found that the mitochondrial genomes of Equus are highly conserved, each encoding 37 genes, including 13 protein-coding genes (PCGs). Phylogenetic analysis based on mitochondrial genomes supports previous research, indicating that the extant species in Equus are divided into three main branches: horses, donkeys, and zebras. Specifically, 761 genetic variants were identified between donkeys and horses, 68 of which were non-synonymous mutations in PCGs, potentially linked to their different locomotor abilities. Structural protein modeling indicated that despite genetic differences, the overall protein structures between donkeys and horses remain similar. This study revealed the mitochondrial genome variation patterns of domesticated animals, offering novelty perspectives on domestication imprints. Additionally, it provides reliable candidate molecular markers for the identification of donkeys and horses.
© 2025. The Author(s).
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Publication Date: 2025-02-25 PubMed ID: 40000832PubMed Central: PMC11861670DOI: 10.1038/s41598-025-91564-1Google Scholar: Lookup
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Summary

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This research article investigates the link between mitochondria and the locomotor abilities in donkeys and horses. It reveals that despite genetic variations, the structural proteins of these animals remain similar, potentially linking to their different locomotor abilities.

Overview of the Research

  • The study focuses on the Equidae family, which includes two domesticated species: donkeys and horses, known respectively for their endurance and power-driven nature.
  • The researchers wanted to explore the correlation between these distinct skills and the animals’ mitochondria – vital organelles that contribute to the energy of animal cells.

Procedure and Findings

  • Six new mitochondrial genomes from donkeys in China were sequenced and assembled as part of the study.
  • In addition, the published mitochondrial genomes of all species within the Equus genus were downloaded and analysed comprehensively.
  • The researchers found that the mitochondrial genomes in Equus are highly conserved, each containing 37 genes, including 13 protein-coding ones.
  • Through phylogenetic analysis, the study confirmed previous research which divided species within the Equus genus into three main branches: horses, donkeys, and zebras.

Distinct Genetic Variations in Donkeys and Horses

  • The study discovered 761 genetic variants between donkeys and horses. Significantly, 68 of these were non-synonymous mutations in protein-coding genes, potentially contributing to their different locomotor abilities.
  • Furthermore, structural protein modeling suggested that despite these genetic differences, the overall protein structures of donkeys and horses remain quite similar.

Implications of the Study

  • The study exposed novel patterns of mitochondrial genome variation in these domesticated animals, providing new perspectives on domestication imprints.
  • It offers potential molecular markers which could distinguish between horses and donkeys reliably.
  • These findings give valuable insight into the genetic mechanisms behind the endurance of donkeys and the power-driven nature of horses, and could influence future breeding programs or genetic modifications for these species.

Cite This Article

APA
Du W, Sun Q, Hu S, Yu P, Kan S, Zhang W. (2025). Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses. Sci Rep, 15(1), 6803. https://doi.org/10.1038/s41598-025-91564-1

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 15
Issue: 1
Pages: 6803
PII: 6803

Researcher Affiliations

Du, Wenchao
  • Marine College, Shandong University, Weihai, 264209, Shandong, China.
Sun, Qifan
  • Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
Hu, Sheng
  • Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
Yu, Pei
  • SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China.
Kan, Shenglong
  • Marine College, Shandong University, Weihai, 264209, Shandong, China. kanshenglong@sdu.edu.cn.
Zhang, Wei
  • Marine College, Shandong University, Weihai, 264209, Shandong, China. wzhang@sdu.edu.cn.

MeSH Terms

  • Animals
  • Equidae / genetics
  • Genome, Mitochondrial
  • Domestication
  • Horses / genetics
  • Phylogeny
  • Genetic Variation
  • Mitochondria / genetics
  • Animals, Domestic / genetics

Grant Funding

  • ZR2023QC278 / Natural Science Foundation of Shandong Province
  • 2022YFC3341002-2 / National Key Research and Development Program of China

Conflict of Interest Statement

Declarations. Competing interests: The authors declare no competing interests. Ethical approval: The animal study protocol was approved by the Institutional Review Board of Institute of Forensic Science, Ministry of Public Security (MPS) (protocol code 2023-002 and approved on 16 Mar. 2023).

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Citations

This article has been cited 2 times.
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