Leadbeater's possum (Gymnobelideus leadbeateri)

Leadbeater's possum were thought to be extinct for half a century until they were rediscovered in the 1960's! Read more about Leadbeater's possums on Animalia's website.

Leadbeater's possum (Gymnobelideus leadbeateri), image by Arabella Eyre, Zoos Victoria

Chromosome-length genome assembly

Download the LBP_v1_HiC.fasta.gz file containing the chromosome-length (2n=22) assembly of the Leadbeater's possum genome. All modifications with respect to the draft (see below) are annotated in the LBP_v1_HiC.assembly file. Some basic stats associated with the new reference, LBP_v1_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly LBP_v1 (GCA_011680675.1), credited below.

This draft genome was produced by collaboration of Zoos Victoria, Monash University and the Deakin Genomics Centre. The draft genome assembly was created using MaSuRCA v. 3.3.4 (Zimin et al. 2013, Bioinformatics 29, 2669-2677), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads. For more details see Gan, H.M., Loke, S., Lee, Y.P., Sunnucks, P. and Pavlova, A. "Leadbeater's possum whole-genome sequencing." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/WOXC00000000.1/.

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 female individual named Dawn, and obtained from Leanne Wicker and Dan Harley (Zoos Victoria).

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 draft genome was produced by collaboration of Zoos Victoria, Monash University and the Deakin Genomics Centre. The draft genome assembly was created using MaSuRCA v. 3.3.4 (Zimin et al. 2013, Bioinformatics 29, 2669-2677), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads. For more details see Gan, H.M., Loke, S., Lee, Y.P., Sunnucks, P. and Pavlova, A. "Leadbeater's possum whole-genome sequencing." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/WOXC00000000.1/.

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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© 2018-2020 by the Aiden Lab.