Improved de novo genomic assembly for the domestic donkey

Gabriel Renaud, Bent Petersen, Andaine Seguin-Orlando, Mads Frost Bertelsen, Andrew Waller, Richard Newton, Romain Paillot, Neil Bryant, Mark Vaudin, Pablo Librado, Ludovic Orlando*

*Corresponding author for this work

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    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.
    Original languageEnglish
    Article numbereaaq0392
    JournalScience Advances
    Volume4
    Issue number4
    Number of pages11
    ISSN2375-2548
    DOIs
    Publication statusPublished - 2018

    Bibliographical note

    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.

    Cite this

    Renaud, G., Petersen, B., Seguin-Orlando, A., Bertelsen, M. F., Waller, A., Newton, R., ... Orlando, L. (2018). Improved de novo genomic assembly for the domestic donkey. Science Advances, 4(4), [eaaq0392]. https://doi.org/10.1126/sciadv.aaq0392
    Renaud, Gabriel ; Petersen, Bent ; Seguin-Orlando, Andaine ; Bertelsen, Mads Frost ; Waller, Andrew ; Newton, Richard ; Paillot, Romain ; Bryant, Neil ; Vaudin, Mark ; Librado, Pablo ; Orlando, Ludovic. / Improved de novo genomic assembly for the domestic donkey. In: Science Advances. 2018 ; Vol. 4, No. 4.
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    title = "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.",
    author = "Gabriel Renaud and Bent Petersen and Andaine Seguin-Orlando and Bertelsen, {Mads Frost} and Andrew Waller and Richard Newton and Romain Paillot and Neil Bryant and Mark Vaudin and Pablo Librado and Ludovic Orlando",
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    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', Science Advances, vol. 4, no. 4, eaaq0392. https://doi.org/10.1126/sciadv.aaq0392

    Improved de novo genomic assembly for the domestic donkey. / Renaud, Gabriel; Petersen, Bent; Seguin-Orlando, Andaine; Bertelsen, Mads Frost ; Waller, Andrew; Newton, Richard ; Paillot, Romain; Bryant, Neil; Vaudin, Mark; Librado, Pablo; Orlando, Ludovic.

    In: Science Advances, Vol. 4, No. 4, eaaq0392, 2018.

    Research output: Contribution to journalJournal articleResearchpeer-review

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    AU - Renaud, Gabriel

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    AU - Paillot, Romain

    AU - Bryant, Neil

    AU - Vaudin, Mark

    AU - Librado, Pablo

    AU - Orlando, Ludovic

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    AB - 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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    Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R et al. Improved de novo genomic assembly for the domestic donkey. Science Advances. 2018;4(4). eaaq0392. https://doi.org/10.1126/sciadv.aaq0392