Improved de novo genomic assembly for the domestic donkey

Research output: Contribution to journalJournal article – Annual report year: 2018Researchpeer-review



  • Author: Renaud, Gabriel

    Natural History Museum of Denmark, Denmark

  • Author: Petersen, Bent

    Metagenomics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Seguin-Orlando, Andaine

    University of Copenhagen, Denmark

  • Author: Bertelsen, Mads Frost

    Copenhagen Zoo, Denmark

  • Author: Waller, Andrew

    Animal Health Trust, United Kingdom

  • Author: Newton, Richard

    Animal Health Trust, United Kingdom

  • Author: Paillot, Romain

    Animal Health Trust, United Kingdom

  • Author: Bryant, Neil

    Animal Health Trust, United Kingdom

  • Author: Vaudin, Mark

    Animal Health Trust, United Kingdom

  • Author: Librado, Pablo

    Natural History Museum of Denmark, Denmark

  • Author: Orlando, Ludovic Antoine Alexandre

    Natural History Museum of Denmark, Denmark

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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.
Original languageEnglish
Article numbereaaq0392
JournalScience Advances
Issue number4
Number of pages11
Publication statusPublished - 2018

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This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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