Leopard cat (Prionailurus bengalensis)

These animals are interbred with domestic cats, yielding a species called Bengal cat, which is globally kept as a house pet. Read more about leopard cats on the Animalia website.

africa-animal-big-cat-88234.jpg

Prionailurus bengalensis by zoologistiques, [CC BY 2.0], via flickr.com

Chromosome-length genome assembly

Download the PriBen1.0.updated_2_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the leopard cat genome. All modifications with respect to the draft (see below) are annotated in the PriBen1.0.updated_2_HiC.assembly file. Some basic stats associated with the new reference, PriBen1.0.updated_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)
2,145,963,998
262,947
16,121
218,745
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,490,745,690
31,824
147,495,894
240,385,465
Draft

The chromosome-length genome assembly is based on the draft assembly PriBen1.0.updated_2 (GCA_018119505.1), credited below.

The assembly is based on based on the PriBen1.0 genome assembly generated and shared via NCBI by A. Komissarov, L. Dalen, A. Wilting and T. Gilbert. The chromosome-length upgrade was done with Hi-C generated using cultured cells from primary fibroblast cell line (passage 4) provided by Polina Perelman (Institute of Molecular and Cellular Biology). Captive male Tuo (PBE-54, NIHAC LC94004) was brought from Tallin Zoo Park (Dr. Vladimir Feinstein) and brought to NIH Asian cats colony. The animal belongs to most Northern euptilura subspecies (Luo et al., 2014, Patel et al., 2017). The cell line was established from skin biopsy by Mary Thompson, in the Laboratory of Genomic Diversity at NCI-Frederick lead by Dr. Stephen O'Brien, and later preserved by Drs. Melody Roelke, Carlos Driscoll, Christina Barr, Stephen Lindell, and David Goldman at the Section of Comparative Behavioral Genomics, NIAAA.Komissarov, A., Dalen, L., Wilting, A. and Gilbert, T. Scaffold-level whole-genome assembly of the leopard cat genome. Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/JACGXU000000000.1/.

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 primary fibroblasts sample for in situ Hi-C preparation was donated by a male individual, and obtained from Polina Perelman.

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.

The assembly is based on based on the PriBen1.0 genome assembly generated and shared via NCBI by A. Komissarov, L. Dalen, A. Wilting and T. Gilbert. The chromosome-length upgrade was done with Hi-C generated using cultured cells from primary fibroblast cell line (passage 4) provided by Polina Perelman (Institute of Molecular and Cellular Biology). Captive male Tuo (PBE-54, NIHAC LC94004) was brought from Tallin Zoo Park (Dr. Vladimir Feinstein) and brought to NIH Asian cats colony. The animal belongs to most Northern euptilura subspecies (Luo et al., 2014, Patel et al., 2017). The cell line was established from skin biopsy by Mary Thompson, in the Laboratory of Genomic Diversity at NCI-Frederick lead by Dr. Stephen O'Brien, and later preserved by Drs. Melody Roelke, Carlos Driscoll, Christina Barr, Stephen Lindell, and David Goldman at the Section of Comparative Behavioral Genomics, NIAAA.Komissarov, A., Dalen, L., Wilting, A. and Gilbert, T. Scaffold-level whole-genome assembly of the leopard cat genome. Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/JACGXU000000000.1/.

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.