Southern marsupial mole (Notoryctes typhlops)

Due to opening backward, the pouch of marsupial moles remains clean from sand as the animal burrows. Read more about southern marsupial moles on Animalia website.

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Photograph by Mike Gillam Copr.2019 California Academy of Sciences

Chromosome-length genome assembly

Download the Notoryctes_typhlops_wtdbg2.shortReadsPolished_HiC.fasta.gz file containing the chromosome-length (2n=20) assembly of the southern marsupial mole genome. All modifications with respect to the draft (see below) are annotated in the Notoryctes_typhlops_wtdbg2.shortReadsPolished_HiC.assembly file. Some basic stats associated with the new reference, Notoryctes_typhlops_wtdbg2.shortReadsPolished_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
3,457,624,070
45,934
139,600
1,043,367
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
3,475,141,070
10,900
317,685,944
670,892,236
Draft

The chromosome-length genome assembly is based on the draft assembly Notoryctes_typhlops_wtdbg2.shortReadsPolished, credited below.

This genome was done as part of a collaboration between the DNA Zoo, the University of Western Australia, and Oz Mammal Genomics. The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using Oxford Nanopore reads generated by the Pask lab at the University of Melbourne and was polished with short-insert size Illumina reads generated by the DNA Zoo team.

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 kidney sample for in situ Hi-C preparation was 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 was done as part of a collaboration between the DNA Zoo, the University of Western Australia, and Oz Mammal Genomics. The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using Oxford Nanopore reads generated by the Pask lab at the University of Melbourne and was polished with short-insert size Illumina reads generated by the DNA Zoo team.

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.