Donkey (Equus asinus)

Unlike horses who will jump or bolt when scared, donkeys will freeze. This has given them the reputation of being very stubborn! Read more about donkeys on LiveScience.

Photo by Couleur from Pixabay

Chromosome-length genome assembly

Download the ASM130575v1_HiC.fasta.gz file containing the chromosome-length (2n=62) assembly of the donkey genome. All modifications with respect to the draft (see below) are annotated in the ASM130575v1_HiC.assembly file. Some basic stats associated with the new reference, ASM130575v1_HiC, are listed below. The full data release can be explored here. Note that chromosome-length genome assembly based on another draft is available for this species, here.

Draft

The chromosome-length genome assembly is based on the draft assembly ASM130575v1 (GCA_001305755.1), credited below.

Jinlong Huang, Yiping Zhao, Dongyi Bai, Wunierfu Shiraigol, Bei Li, Lihua Yang, Jing Wu, et al. 2015. "Donkey Genome and Insight into the Imprinting of Fast Karyotype Evolution." Scientific Reports 5 (September): 14106. https://doi.org/10.1038/srep14106.

Method

3D Assembly was performed using 3D-DNA pipeline (Dudchenko et al., Science, 2017). The genome was reviewed using Juicebox Assembly Tools  (Dudchenko et al., bioRxiv, 2018). See Methods for more information.

Hi-C sample

The blood sample for in situ Hi-C preparation was donated by a male individual, and provided to us by Animal Technologies.

Hi-C Contact maps

Hi-C data was aligned to the draft reference using Juicer (Durand, Shamim et al., Cell Systems, 2016), and contact maps visualizing the alignments with respect to the draft and the new reference were built using 3D-DNA (Dudchenko et al., Science, 2017). The contact maps can be explored below via Juicebox.js interactive tool (Robinson et al., Cell Systems, 2018). (Please note that the interactive figures are scaled 1:2.) To explore the assembly in greater detail, please download the .hic and .assembly files from the data release folder and use Juicebox Assembly Tools  (Dudchenko et al., bioRxiv, 2018).

References

If you use this genome assembly in your research, please check that the conditions of use associated with the draft permit it, and acknowledge the following work.

Jinlong Huang, Yiping Zhao, Dongyi Bai, Wunierfu Shiraigol, Bei Li, Lihua Yang, Jing Wu, et al. 2015. "Donkey Genome and Insight into the Imprinting of Fast Karyotype Evolution." Scientific Reports 5 (September): 14106. https://doi.org/10.1038/srep14106.

Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.

Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.

Disclaimer

This is a work in progress. If you notice any discrepancies in the map or have data that confirms or contradicts the suggested reference, please email us at theaidenlab@gmail.com or leave a comment on the Forum.

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© 2018-2019 by the Aiden Lab.