Black swan (Cygnus atratus)

Like other swans, the black swan is largely monogamous, pairing for life with about 6% divorce rate. Read more about black swans on Wikipedia.

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Australian black swan, photo by Parwinder Kaur [CC].

Chromosome-length genome assembly

Download the Cygnus_atratus_primary_v1.0_HiC.fasta.gz file containing the chromosome-length assembly of the the black swan genome. All modifications with respect to the draft (see below) are annotated in the Cygnus_atratus_primary_v1.0_HiC.assembly file. Some basic stats associated with the new reference, Cygnus_atratus_primary_v1.0_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
1,122,279,392
1,070
7,459,382
29,909,885
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
1,122,530,392
568
84,263,156
208,757,806
Draft

The chromosome-length genome assembly is based on the draft assembly Cygnus_atratus_primary_v1.0 (GCF_013377495.1), credited below.

This genome assembly was done in collaboration with Prof. Dave Burt, Dr. Kirsty Short and Anjana Karawita at the University of Queensland, Australia. The PacBio draft assembly, publicly available on NCBI, was created by the University of Queensland team, led by Dr Kirsty Short and PhD candidate Anjana Karawita. For details see https://www.ncbi.nlm.nih.gov/nuccore/JABXOC000000000.1..

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 stomach muscle wall sample for in situ Hi-C preparation was donated by a male individual, and obtained from Anjana Karawita (University of Queensland). We thank SeaWorld for additional samples for this species.

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). 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 done in collaboration with Prof. Dave Burt, Dr. Kirsty Short and Anjana Karawita at the University of Queensland, Australia. The PacBio draft assembly, publicly available on NCBI, was created by the University of Queensland team, led by Dr Kirsty Short and PhD candidate Anjana Karawita. For details see https://www.ncbi.nlm.nih.gov/nuccore/JABXOC000000000.1..

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 thednazoo@gmail.com or leave a comment on the Forum.