Southern right whale (Eubalaena australis)

Nineteenth century whaling almost wiped out all southern right whales in Australian waters. An estimated 55,000 to 70,000 cruised the Southern Hemisphere in the late 1700s. By the 1920s, fewer than 300 remained. Now listed as endangered under the Environment Protection and Biodiversity Conservation (EPBC) Act 1999, protection measures have seen numbers increase to an estimated 3,500 individuals. Read more about southern right whales on the World Wide Fund for Nature (WWF) website.

Eubalaena australis (Southern right whale) by Dr. Emma Louise Carroll, University of Auckland, Taken under Department of Conservation permit

Chromosome-length genome assembly

Download the RWref_HiC.fasta.gz file containing the chromosome-length (2n=42) assembly of the southern right whale genome. All modifications with respect to the draft (see below) are annotated in the RWref_HiC.assembly file. Some basic stats associated with the new reference, RWref_HiC, are listed below. The full data release can be explored here.

Draft

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

The draft genome assembly was generated by Mark Yandell's lab at the University of Utah with contributions from Michael S. Campbell, Brian Dalley, Edgar J. Hernandez, Barry Moore, Andrea Chirife, Matias Di Martino, Mariano Sironi, Luciano O. Valenzuela, Marcela Uhart, Victoria J. Rowntree, Guy D. Eroh, Sancy A. Leachman and Jon Seger. Construction of the draft was funded and supported by the Illumina Corporation, by the H.A. and Edna Benning Fund, and by the US National Science 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 skin sample for in situ Hi-C preparation was donated by a female individual, and obtained from Emma Caroll (University of Auckland).

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.

The draft genome assembly was generated by Mark Yandell's lab at the University of Utah with contributions from Michael S. Campbell, Brian Dalley, Edgar J. Hernandez, Barry Moore, Andrea Chirife, Matias Di Martino, Mariano Sironi, Luciano O. Valenzuela, Marcela Uhart, Victoria J. Rowntree, Guy D. Eroh, Sancy A. Leachman and Jon Seger. Construction of the draft was funded and supported by the Illumina Corporation, by the H.A. and Edna Benning Fund, and by the US National Science 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 theaidenlab@gmail.com or leave a comment on the Forum.

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© 2018-2020 by the Aiden Lab.