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Red-bellied piranha (Pygocentrus nattereri)

Red-bellied piranha is the most common aquarium piranha. These piranhas bark when angered! Read more about red-bellied piranhas on Wikipedia.


"Red Piranhas" by Stig Nygaard [CC BY 2.0], via

Chromosome-length genome assembly

Download the Pygocentrus_nattereri-1.0.2_HiC.fasta.gz file containing the chromosome-length (2n=60) assembly of the red-bellied piranha genome. All modifications with respect to the draft (see below) are annotated in the Pygocentrus_nattereri-1.0.2_HiC.assembly file. Some basic stats associated with the new reference, Pygocentrus_nattereri-1.0.2_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)

The chromosome-length genome assembly is based on the draft assembly Pygocentrus_nattereri-1.0.2 (GCF_001682695.1), credited below.

Warren, W.C. and Schartl, M. "The Pygocentrus nattereri whole genome shotgun (WGS) project." Unpublished.


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 sample for in situ Hi-C preparation was provided to us by Moody Gardens.

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).


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.

Warren, W.C. and Schartl, M. "The Pygocentrus nattereri whole genome shotgun (WGS) project." Unpublished.

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.

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.


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 or leave a comment on the Forum.

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