Koala (Phascolarctos cinereus)

Koalas can consume up to 1 lb of toxic eucalyptus leaves a day. Despite the koala's enormus appetite for eucalyptus, they recieve very little nutrition after the extensive digestion process. It's no wonder koalas sleep 18-22 hours a day! Read more about koalas on National Geographic's website.

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Koala (Phascolarctos cinereus) Photo Credits & acknowledgements - Parwinder Kaur, [CC BY 2.0]

Chromosome-length genome assembly

Download the phaCin_unsw_v4.1_HiC.fasta.gz file containing the chromosome-length (2n=16) assembly of the koala genome. All modifications with respect to the draft (see below) are annotated in the phaCin_unsw_v4.1_HiC.assembly file. Some basic stats associated with the new reference, phaCin_unsw_v4.1_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
3,192,581,491
1,936
11,399,805
40,558,015
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
3,192,889,992
1,318
480,107,551
730,168,553
Draft

The chromosome-length genome assembly is based on the draft assembly phaCin_unsw_v4.1 (GCF_002099425.1), credited below.

Johnson, R.N., O'Meally, D., Chen, Z., Etherington, G.J., Ho, S.Y.W., Nash, W.J., Grueber, C.E., Cheng, Y., Whittington, C.M., Dennison, S., Peel, E., Haerty, W., O'Neill, R.J., Colgan, D., Russell, T.L., Alquezar-Planas, D.E., Attenbrow, V., Bragg, J.G., Brandies, P.A., Chong, A.Y.-Y., Deakin, J.E., Di Palma, F., Duda, Z., Eldridge, M.D.B., Ewart, K.M., Hogg, C.J., Frankham, G.J., Georges, A., Gillett, A.K., Govendir, M., Greenwood, A.D., Hayakawa, T., Helgen, K.M., Hobbs, M., Holleley, C.E., Heider, T.N., Jones, E.A., King, A., Madden, D., Graves, J.A.M., Morris, K.M., Neaves, L.E., Patel, H.R., Polkinghorne, A., Renfree, M.B., Robin, C., Salinas, R., Tsangaras, K., Waters, P.D., Waters, S.A., Wright, B., Wilkins, M.R., Timms, P., Belov, K., 2018. Adaptation and conservation insights from the koala genome. Nat. Genet. 50, 1102-1111. https://doi.org/10.1038/s41588-018-0153-5.

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 heart sample for in situ Hi-C preparation was donated by a male individual, and obtained from Ranger Red's Zoo & Conservation Park/Bradley R Holland.

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.

Johnson, R.N., O'Meally, D., Chen, Z., Etherington, G.J., Ho, S.Y.W., Nash, W.J., Grueber, C.E., Cheng, Y., Whittington, C.M., Dennison, S., Peel, E., Haerty, W., O'Neill, R.J., Colgan, D., Russell, T.L., Alquezar-Planas, D.E., Attenbrow, V., Bragg, J.G., Brandies, P.A., Chong, A.Y.-Y., Deakin, J.E., Di Palma, F., Duda, Z., Eldridge, M.D.B., Ewart, K.M., Hogg, C.J., Frankham, G.J., Georges, A., Gillett, A.K., Govendir, M., Greenwood, A.D., Hayakawa, T., Helgen, K.M., Hobbs, M., Holleley, C.E., Heider, T.N., Jones, E.A., King, A., Madden, D., Graves, J.A.M., Morris, K.M., Neaves, L.E., Patel, H.R., Polkinghorne, A., Renfree, M.B., Robin, C., Salinas, R., Tsangaras, K., Waters, P.D., Waters, S.A., Wright, B., Wilkins, M.R., Timms, P., Belov, K., 2018. Adaptation and conservation insights from the koala genome. Nat. Genet. 50, 1102-1111. https://doi.org/10.1038/s41588-018-0153-5.

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.