Nothern quoll (Dasyurus hallucatus)

The Northern quoll is the smallest of the four Australian quoll species. Read more about nothern quoll on Australian Wildlife Conservancy (AWC) website.

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Northern quoll, photo by S J Bennett, CC BY-NC 2.0, via flickr.com

Chromosome-length genome assembly

Download the Dasyurus_hallucatus_10X_01_style3pseudohapfull_HiC.fasta.gz file containing the chromosome-length (2n=14) assembly of the nothern quoll genome. All modifications with respect to the draft (see below) are annotated in the Dasyurus_hallucatus_10X_01_style3pseudohapfull_HiC.assembly file. Some basic stats associated with the new reference, Dasyurus_hallucatus_10X_01_style3pseudohapfull_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
3,086,652,258
479,471
91,016
673,453
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
3,148,303,998
418,623
605,074,943
704,032,910
Draft

The chromosome-length genome assembly is based on the draft assembly Dasyurus_hallucatus_10X_01_style3pseudohapfull, credited below.

This genome assembly is a collaborative effort of DNA Zoo labs with Assoc. Prof. Ben Phillips and Dr. Stephen Frankenberg from the University of Melbourne along with Dr. Adnan Moussalli from Museums Victoria. The chromosome-length assembly is based on a draft assembly produced using 10x Genomics Chromium linked-read sequencing of a male northern quoll fibroblast cell line, established from a tissue sample kindly provided by the Territory Wildlife Park, and assembled using the Supernova assembler with additional funding from the Hermon-Slade Foundation.

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 liver sample for in situ Hi-C preparation was donated by a male individual, and obtained from Stephen Frankenberg (University of Melbourne).

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.

This genome assembly is a collaborative effort of DNA Zoo labs with Assoc. Prof. Ben Phillips and Dr. Stephen Frankenberg from the University of Melbourne along with Dr. Adnan Moussalli from Museums Victoria. The chromosome-length assembly is based on a draft assembly produced using 10x Genomics Chromium linked-read sequencing of a male northern quoll fibroblast cell line, established from a tissue sample kindly provided by the Territory Wildlife Park, and assembled using the Supernova assembler with additional funding from the Hermon-Slade Foundation.

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 thednazoo@gmail.com or leave a comment on the Forum.