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Home / Equine Research Bank / Sci Adv / Improved de novo genomic assembly for the domestic donkey.
Science advances2018; 4(4); eaaq0392; doi: 10.1126/sciadv.aaq0392

Improved de novo genomic assembly for the domestic donkey.

Abstract: Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.
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Publication Date: 2018-04-04 PubMed ID: 29740610PubMed Central: PMC5938232DOI: 10.1126/sciadv.aaq0392Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research paper discusses an improved genome assembly for domestic donkey, obtained using the Chicago HiRise assembly technology to analyze genomic variations and chromosomal rearrangements. This features a more precise measure of heterozygosity and possible signs of positive selection among domestic donkeys.

Introduction

  • The study primarily revolves around a new high-quality genome assembly for the domestic donkey, which was acquired using the Chicago HiRise assembly technology.
  • The research work emphasizes the importance of this new genome assembly, as previous ones were limited and hampered studies involving the characterization of patterns of genetic variation.
  • The absence of an efficient quality assembly hindered the application of genomic tools for selective breeding, conservation, and characterizing genomic loci underlying speciation and domestication.

Genome Assembly

  • The robust assembly technology of Chicago HiRise has been instrumental in obtaining high-quality donkey genome assembly.
  • The assembly process offers scaffolds of subchromosomal size, increasing the structure’s precision and clarity.
  • The report also mentions how this upgraded assembly could lead to more accurate measures of heterozygosity for equines other than horses, both genome-wide and locally.

Detection of Patterns

  • This upgraded genome assembly has also been helpful in detecting runs of homozygosity in domestic donkeys; this could potentially indicate areas of positive selection.
  • Positive selection is a vital process in the evolution of species, indicating survival benefits achieved from certain gene variations.

Identification of Chromosomal Rearrangements

  • The new genome assembly enabled researchers to identify fine-scale chromosomal rearrangements between donkeys and horses.
  • These chromosomal rearrangements likely played an active role in their divergence, and ultimately, speciation, evolving from a common ancestor about four million years ago.

Concluding Notes

  • In summary, the research marks a significant step forward in understanding the genomic architecture and evolution of donkeys, which had previously been limited due to inferior quality genome assembly methods.
  • The use of Chicago HiRise assembly technology could pave the way for similar study upgrades in other species, helping scientists identify genetic variations and understand chromosomal rearrangements, ultimately leading to a more profound comprehension of speciation and evolution.

Cite This Article

APA
Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. (2018). Improved de novo genomic assembly for the domestic donkey. Sci Adv, 4(4), eaaq0392. https://doi.org/10.1126/sciadv.aaq0392

Publication

Science advances
ISSN: 2375-2548
NlmUniqueID: 101653440
Country: United States
Language: English
Volume: 4
Issue: 4
Pages: eaaq0392
PII: eaaq0392

Researcher Affiliations

Renaud, Gabriel
  • Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.
Petersen, Bent
  • DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah, Malaysia.
Seguin-Orlando, Andaine
  • Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.
  • National High-Throughput DNA Sequencing Center, Copenhagen, Denmark.
  • Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France.
Bertelsen, Mads Frost
  • Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
Waller, Andrew
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
Newton, Richard
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
Paillot, Romain
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
Bryant, Neil
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
Vaudin, Mark
  • Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK.
Librado, Pablo
  • Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.
  • Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France.
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.
  • Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthése UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, 31000 Toulouse, France.

MeSH Terms

  • Animals
  • Animals, Domestic
  • Computational Biology / methods
  • DNA, Mitochondrial
  • Equidae / classification
  • Equidae / genetics
  • Genetic Variation
  • Genome
  • Genomics / methods
  • Heterozygote
  • Homozygote
  • Molecular Sequence Annotation

Grant Funding

  • European Research Council

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