Spotted owl (Strix occidentalis)

When faced with more food than they can eat, spotted owls may cache prey. An owl that has just cached prey will sit upright, stare at the cached food, then slowly back away from it on foot, as if to fix the location in its mind! Read more about spotted owls on All About Birds website.

Strix occidentalis caurina, Northern Spotted Owl, by Frank D. Lospalluto [CC BY-NC-ND 2.0], via flickr.com

Chromosome-length genome assembly

Download the Strix_occidentalis_HiC.fasta.gz file containing the chromosome-length assembly of the spotted owl genome. All modifications with respect to the draft (see below) are annotated in the Strix_occidentalis_HiC.assembly file. Some basic stats associated with the new reference, Strix_occidentalis_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly Strix_occidentalis, credited below.

We thank Zach Hanna (UCSF), Jack Dumbacher (California Academy of Sciences), Michal Levy-Sakin (Dovetail Genomics), Rauri Bowie (UC Berkeley), Pui Kwok (UCSF) and Jeff Wall (UCSF) for donating data associated with this assembly and generating the draft genome assembly.

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

Hi-C data for this assembly was generated by Zach Hanna (UCSF), Jack Dumbacher (California Academy of Sciences), Michal Levy-Sakin (Dovetail Genomics), Rauri Bowie (UC Berkeley), Pui Kwok (UCSF) and Jeff Wall (UCSF).

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.

We thank Zach Hanna (UCSF), Jack Dumbacher (California Academy of Sciences), Michal Levy-Sakin (Dovetail Genomics), Rauri Bowie (UC Berkeley), Pui Kwok (UCSF) and Jeff Wall (UCSF) for donating data associated with this assembly and generating the draft genome assembly.

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.