Yellowfin tuna (Thunnus albacares)

Yellowfin tuna form schools with other tunas like skipjack and bigeye, and are also known to associate with dolphins! Read more about yellowfin tuna on WWF website.

OAR/National Undersea Research Program (NURP), Public domain, via Wikimedia Commons, https://commons.wikimedia.org/wiki/File:Yellowfin_tuna_nurp.jpg

Chromosome-length genome assembly

Download the ASM90030262v1.fasta.gz file containing the chromosome-length (2n=48) assembly of the yellowfin tuna genome. All modifications with respect to the draft (see below) are annotated in the ASM90030262v1.assembly file. Some basic stats associated with the new reference, ASM90030262v1, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly ASM90030262v1 (GCA_900302625.1), credited below.

Malmstrøm, M., Matschiner, M., Tørresen, O.K., Jakobsen, K.S., Jentoft, S., 2017. Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Sci. Data 4. https://doi.org/10.1038/sdata.2016.132.

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 muscle sample for in situ Hi-C preparation was obtained from Pierre Feuty (CSIRO, Hobart).

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.

Malmstrøm, M., Matschiner, M., Tørresen, O.K., Jakobsen, K.S., Jentoft, S., 2017. Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Sci. Data 4. https://doi.org/10.1038/sdata.2016.132.

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.