Jaguarundi (Herpailurus yagouaroundi)

The jaguarundi are quite small as compared to other New World wild cats; they are only twice as large as domestic cats! Read more about jaguarundis on Wikipedia.

africa-animal-big-cat-88234.jpg

Jaguarundi ( Puma yagouaroundi ) au zoo de Pont-Scorff by Vassil, [CC0 1.0], via wikimedia.org

Chromosome-length genome assembly

Download the jaguarundi_pseudohap2.1.filtered_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the jaguarundi genome. All modifications with respect to the draft (see below) are annotated in the jaguarundi_pseudohap2.1.filtered_HiC.assembly file. Some basic stats associated with the new reference, jaguarundi_pseudohap2.1.filtered_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,419,743,964
53,512
100,150
766,737
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,469,288,098
10,570
148,011,704
241,402,989
Draft

The chromosome-length genome assembly is based on the draft assembly jaguarundi_pseudohap2.1.filtered, credited below.

Tamazian, G., Dobrynin, P., Zhuk, A., Zhernakova, D.V., Perelman, P.L., Serdyukova, N.A., Graphodatsky, A.S., Komissarov, A., Kliver, S., Cherkasov, N., Scott, A.F., Mohr, D.W., Koepfli, K.-P., O'Brien, S.J., Krasheninnikova, K., 2021. Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi. J. Hered. https://doi.org/10.1093/jhered/esab036.

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 Kunming Cell Bank of the Chinese Academy of Sciences, Kunming, Yunnan, China, through Drs. Malcolm Ferguson-Smith and Fengtang Yang at Department of Veterinary Medicine, University of Cambridge, UK to Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky).

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.

Tamazian, G., Dobrynin, P., Zhuk, A., Zhernakova, D.V., Perelman, P.L., Serdyukova, N.A., Graphodatsky, A.S., Komissarov, A., Kliver, S., Cherkasov, N., Scott, A.F., Mohr, D.W., Koepfli, K.-P., O'Brien, S.J., Krasheninnikova, K., 2021. Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi. J. Hered. https://doi.org/10.1093/jhered/esab036.

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.