American black bear (Ursus americanus)

Black bears have a bit of a misleading name. Black bears can also be brown, cinnamon or blonde. And black bears in a small population in coastal British Columbia, the Kermode bears, are actually completely white! Read more about American black bears in Wikipedia.

By Ryan E. Poplin (originally posted to Flickr as Black Bear #7) [CC BY-SA 2.0 (https://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

Chromosome-length genome assembly

Download the ASM334442v1_HiC.fasta.gz file containing the chromosome-length (2n=74) assembly of the American black bear genome. All modifications with respect to the draft (see below) are annotated in the ASM334442v1_HiC.assembly file. Some basic stats associated with the new reference, ASM334442v1_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly ASM334442v1 (GCA_003344425.1), credited below.

Srivastava, Anuj, Vishal Kumar Sarsani, Ian Fiddes, Susan M. Sheehan, Rita L. Seger, Mary E. Barter, Selena Neptune-Bear, Charlotte Lindqvist, and Ron Korstanje. 2018. "Genome Assembly and Gene Expression in the American Black Bear Provides New Insights into the Renal Response to Hibernation." DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, November. https://doi.org/10.1093/dnares/dsy036.

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 named Willow, and provided to us by Houston Zoo. We thank San Antonio Zoo and OKC Zoo for additional american black bear samples.

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.

Srivastava, Anuj, Vishal Kumar Sarsani, Ian Fiddes, Susan M. Sheehan, Rita L. Seger, Mary E. Barter, Selena Neptune-Bear, Charlotte Lindqvist, and Ron Korstanje. 2018. "Genome Assembly and Gene Expression in the American Black Bear Provides New Insights into the Renal Response to Hibernation." DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, November. https://doi.org/10.1093/dnares/dsy036.

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.