Fat-tailed dunnart (Sminthopsis crassicaudata)

During periods of abundant food, fat-tailed dunnarts store fat in their tails. These fat stores allow dunnarts to survive food shortages. Their tails become thinner during the winder. Read more about fat-tailed dunnart on Animalia website.

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Fat-tailed Dunnart (Sminthopsis crassicaudata) by Bernard Dupont, [CC BY-NC 2.0], via creativecommons.org

Chromosome-length genome assembly

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

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,801,635,494
3,049
8,525,256
33,669,817
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,836,947,424
1,644
578,922,139
631,029,432
Draft

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

This genome assembly was generated using an unpublished draft assembly generated by the University of Melbourne team, led by Prof. Andrew Pask. The effort has been supported by an ARC grant (DP160103683) to Pask and Frankenberg and Oz Mammals Genomics initiative, a Bioplatforms Australia

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 was generated using an unpublished draft assembly generated by the University of Melbourne team, led by Prof. Andrew Pask. The effort has been supported by an ARC grant (DP160103683) to Pask and Frankenberg and Oz Mammals Genomics initiative, a Bioplatforms Australia

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.