Brownbanded bamboo shark (Chiloscyllium punctatum)

The shark got its name from the dark brown bands around its body. Actually, it is deep brown over light brown body! The color contrast is high in the juveniles but fades in adults. Read more about brownbanded bamboo sharks on Wikipedia.

africa-animal-big-cat-88234.jpg

Steve Childs / CC BY (https://creativecommons.org/licenses/by/2.0), via wikimedia.org

Chromosome-length genome assembly

Download the Cpunctatum_v1.0_HiC.fasta.gz file containing the chromosome-length (2n=104) assembly of the brownbanded bamboo shark genome. All modifications with respect to the draft (see below) are annotated in the Cpunctatum_v1.0_HiC.assembly file. Some basic stats associated with the new reference, Cpunctatum_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)
3,043,880,664
467,967
20,714
346,695
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
3,377,889,642
275,693
69,917,805
153,865,261
Draft

The chromosome-length genome assembly is based on the draft assembly Cpunctatum_v1.0 (GCA_003427335.1), credited below.

Hara, Y., Yamaguchi, K., Onimaru, K., Kadota, M., Koyanagi, M., Keeley, S.D., Tatsumi, K., Tanaka, K., Motone, F., Kageyama, Y., Nozu, R., Adachi, N., Nishimura, O., Nakagawa, R., Tanegashima, C., Kiyatake, I., Matsumoto, R., Murakumo, K., Nishida, K., Terakita, A., Kuratani, S., Sato, K., Hyodo, S., Kuraku, S., 2018. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nat. Ecol. Evol. 2, 1761-1771. https://doi.org/10.1038/s41559-018-0673-5.

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 blood sample for in situ Hi-C preparation was donated by a male individual, and provided to us by SeaWorld.

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.

Hara, Y., Yamaguchi, K., Onimaru, K., Kadota, M., Koyanagi, M., Keeley, S.D., Tatsumi, K., Tanaka, K., Motone, F., Kageyama, Y., Nozu, R., Adachi, N., Nishimura, O., Nakagawa, R., Tanegashima, C., Kiyatake, I., Matsumoto, R., Murakumo, K., Nishida, K., Terakita, A., Kuratani, S., Sato, K., Hyodo, S., Kuraku, S., 2018. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nat. Ecol. Evol. 2, 1761-1771. https://doi.org/10.1038/s41559-018-0673-5.

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.