Gray short-tailed opossum (Monodelphis domestica)

Newborn opossums can heal complete transections of the spinal cord! Understanding the underlying mechanisms may prove useful for regenerative medicine studies. Read more about gray short-tailed opossums in Wikipedia.

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Chromosome-length genome assembly

Download the MonDom5_HiC.fasta.gz file containing the chromosome-length (2n=18) assembly of the gray short-tailed opossum genome. All modifications with respect to the draft (see below) are annotated in the MonDom5_HiC.assembly file. Some basic stats associated with the new reference, MonDom5_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly MonDom5 (GCF_000002295.2), credited below.

Mikkelsen, Tarjei S., Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke, Manuel Garber, et al. 2007. "Genome of the Marsupial Monodelphis Domestica Reveals Innovation in Non-Coding Sequences." Nature 447 (7141): 167-77. https://doi.org/10.1038/nature05805.

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 female individual, and provided to us by Bluma Lesch, Yale. We thank Gunter Wagner Lab/Yale for additional samples for this species.

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.

Mikkelsen, Tarjei S., Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke, Manuel Garber, et al. 2007. "Genome of the Marsupial Monodelphis Domestica Reveals Innovation in Non-Coding Sequences." Nature 447 (7141): 167-77. https://doi.org/10.1038/nature05805.

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.