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Pacific white-sided dolphin (Lagenorhynchus obliquidens)

Different species of dolphins have varied jumping abilities, with the Pacific white-sided dolphin probably getting the grand prize for height. It can jump 30 feet above the water! Read more about Pacific white-sided dolphins on American Cetacean Society website.

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Photo by Robin Agarwal "Pacific White-sided Dolphin (Lagenorhynchus obliquidens)" [CC BY-NC 2.0 (https://creativecommons.org/licenses/by-nc/2.0/)], via flickr.com

Chromosome-length genome assembly

Download the ASM367639v1_HiC.fasta.gz file containing the chromosome-length (2n=44) assembly of the Pacific white-sided dolphin genome. All modifications with respect to the draft (see below) are annotated in the ASM367639v1_HiC.assembly file. Some basic stats associated with the new reference, ASM367639v1_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,324,171,299
21,805
255,779
1,515,302
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,333,909,671
5,162
107,447,310
180,730,733
Draft

The chromosome-length genome assembly is based on the draft assembly ASM367639v1 (GCF_003676395.1), credited below.

Culibrk,L., Leelakumari,S., Taylor,G.A., Tan,R., Tse,K., Cheng,D., Chuah,E., Kirk,H., Macleod,T., Pandoh,P., Troussard,A., Zhao,Y., Mungall,A.J., Moore,R., Marra,M.A., Haulena,M. and Jones,S.J.M. "The genome of the whitesided dolphin." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/RCWK00000000.1.

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 blood sample for in situ Hi-C preparation was donated by a female individual named Piquet, and provided to us by Shedd Aquarium. 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). (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.

Culibrk,L., Leelakumari,S., Taylor,G.A., Tan,R., Tse,K., Cheng,D., Chuah,E., Kirk,H., Macleod,T., Pandoh,P., Troussard,A., Zhao,Y., Mungall,A.J., Moore,R., Marra,M.A., Haulena,M. and Jones,S.J.M. "The genome of the whitesided dolphin." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/RCWK00000000.1.

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.

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