Pygmy sperm whale (Kogia breviceps)
Like squid, pygmy sperm whales are able to produce a dark ink-like liquid, helping them to escape from predators! Read more about pygmy sperm whales on NOAA Fisheries website.
Pygmy sperm whale (Kogia breviceps); Rescued in accordance with NOAA's Marine Mammal Health and Stranding Response Program MMHSRP Permit #18786-04
Chromosome-length genome assembly
Download the KogBre_v1_BIUU_HiC.fasta.gz file containing the chromosome-length (2n=42) assembly of the pygmy sperm whale genome. All modifications with respect to the draft (see below) are annotated in the KogBre_v1_BIUU_HiC.assembly file. Some basic stats associated with the new reference, KogBre_v1_BIUU_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,759,092,859 | 1,258,527 | 26,116 | 437,878 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,782,744,659 | 1,206,381 | 69,986,930 | 160,851,542 |
Draft
The chromosome-length genome assembly is based on the draft assembly KogBre_v1_BIUU (GCA_004363705.1), credited below.
Genereux, D.P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V.D., Murén, E., Juan, D., Bejerano, G., Casewell, N.R., Chemnick, L.G., Damas, J., Di Palma, F., Diekhans, M., Fiddes, I.T., Garber, M., Gladyshev, V.N., Goodman, L., Haerty, W., Houck, M.L., Hubley, R., Kivioja, T., Koepfli, K.-P., Kuderna, L.F.K., Lander, E.S., Meadows, J.R.S., Murphy, W.J., Nash, W., Noh, H.J., Nweeia, M., Pfenning, A.R., Pollard, K.S., Ray, D.A., Shapiro, B., Smit, A.F.A., Springer, M.S., Steiner, C.C., Swofford, R., Taipale, J., Teeling, E.C., Turner-Maier, J., Alfoldi, J., Birren, B., Ryder, O.A., Lewin, H.A., Paten, B., Marques-Bonet, T., Lindblad-Toh, K., Karlsson, E.K., Zoonomia Consortium, 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240-245. https://doi.org/10.1038/s41586-020-2876-6.
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, and obtained from 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.
Genereux, D.P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V.D., Murén, E., Juan, D., Bejerano, G., Casewell, N.R., Chemnick, L.G., Damas, J., Di Palma, F., Diekhans, M., Fiddes, I.T., Garber, M., Gladyshev, V.N., Goodman, L., Haerty, W., Houck, M.L., Hubley, R., Kivioja, T., Koepfli, K.-P., Kuderna, L.F.K., Lander, E.S., Meadows, J.R.S., Murphy, W.J., Nash, W., Noh, H.J., Nweeia, M., Pfenning, A.R., Pollard, K.S., Ray, D.A., Shapiro, B., Smit, A.F.A., Springer, M.S., Steiner, C.C., Swofford, R., Taipale, J., Teeling, E.C., Turner-Maier, J., Alfoldi, J., Birren, B., Ryder, O.A., Lewin, H.A., Paten, B., Marques-Bonet, T., Lindblad-Toh, K., Karlsson, E.K., Zoonomia Consortium, 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240-245. https://doi.org/10.1038/s41586-020-2876-6.
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.