Rock hyrax (Procavia capensis)

Hyraxes may look like rodents, but they are in fact closely related to elephants and manatees. They even have tusks! Read more about rock hyraxes in Wired.

Photo by Tacman10 from Pixabay

Chromosome-length genome assembly

Download the Pcap_2.0_HiC.fasta.gz file containing the chromosome-length (2n=54) assembly of the rock hyrax genome. All modifications with respect to the draft (see below) are annotated in the Pcap_2.0_HiC.assembly file. Some basic stats associated with the new reference, Pcap_2.0_HiC, are listed below. The full data release can be explored here. Note that chromosome-length genome assembly based on another draft is available for this species, here.

Draft

The chromosome-length genome assembly is based on the draft assembly Pcap_2.0 (GCA_000152225.2), credited below.

These are improved versions of the contigs from Lindblad-Toh, Kerstin, Manuel Garber, Or Zuk, Michael F. Lin, Brian J. Parker, Stefan Washietl, Pouya Kheradpour, et al. 2011. "A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals." Nature 478 (7370): 476-82, funded by NHGRI grant HG003273 to Richard Gibbs, by Liu,Y., Qu,J., Gnerre,S., Cree,A., Dinh,H., Dugan,S., Jhangiani,S., Lee,S.L., Nazareth,L., Okwuonu,G., Santibanez,J., Anosike,U., Bandaranaike,D., Bickham,C., Chao,H., Chavez,A., Dahdouli,M., Dao,M., Davila,M., Davy-Carroll,L., Denson,S., Falls,T., Fernandez,S., Fernando,P., Francis,C., Ganer,J., Garcia,R. III, Gross,S., Hale,W., Heiman,D., Hollins,B., Javaid,M., Johnson,B., Jones,J., Joshi,V., Kalu,J., Kisamo,H., Largo,L., Le,T., Leal,B., Legall,F. III, Lemon,S., Lewis,L., Lopez,J., Martinez,E., Matakis,S., Mercado,I., Munidasa,M., Narasimhan,A., Ng,B., Ngo,D., Nguyen,L., Obregon,M., Ongeri,F., Onwere,C., Osuji,N., Parra,A., Perez,A., Perez,Y., Pham,C., Primus,E., Puazo,R., Qi,S., Qu,C., Quiroz,J., Raj,R., Rajbhandari,K., Ruiz,S., Schneider,B., Simmons,D., Sisson,I., Skinner,E., Thornton,R., Usmani,K., Walker,D., White,C., Williams,A., Woodworth,J., Wright,R., Young,S., Yun,X., Han,Y., Kovar,C., Reid,J.G., Weinstock,G., Doddapaneni,H., Muzny,D.M., Worley,K.C. and Gibbs,R.A. https://www.ncbi.nlm.nih.gov/nuccore/ABRQ00000000.

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 male individual, and provided to us by San Antonio Zoo. We thank SeaWorld for additional samples for this species.

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.

These are improved versions of the contigs from Lindblad-Toh, Kerstin, Manuel Garber, Or Zuk, Michael F. Lin, Brian J. Parker, Stefan Washietl, Pouya Kheradpour, et al. 2011. "A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals." Nature 478 (7370): 476-82, funded by NHGRI grant HG003273 to Richard Gibbs, by Liu,Y., Qu,J., Gnerre,S., Cree,A., Dinh,H., Dugan,S., Jhangiani,S., Lee,S.L., Nazareth,L., Okwuonu,G., Santibanez,J., Anosike,U., Bandaranaike,D., Bickham,C., Chao,H., Chavez,A., Dahdouli,M., Dao,M., Davila,M., Davy-Carroll,L., Denson,S., Falls,T., Fernandez,S., Fernando,P., Francis,C., Ganer,J., Garcia,R. III, Gross,S., Hale,W., Heiman,D., Hollins,B., Javaid,M., Johnson,B., Jones,J., Joshi,V., Kalu,J., Kisamo,H., Largo,L., Le,T., Leal,B., Legall,F. III, Lemon,S., Lewis,L., Lopez,J., Martinez,E., Matakis,S., Mercado,I., Munidasa,M., Narasimhan,A., Ng,B., Ngo,D., Nguyen,L., Obregon,M., Ongeri,F., Onwere,C., Osuji,N., Parra,A., Perez,A., Perez,Y., Pham,C., Primus,E., Puazo,R., Qi,S., Qu,C., Quiroz,J., Raj,R., Rajbhandari,K., Ruiz,S., Schneider,B., Simmons,D., Sisson,I., Skinner,E., Thornton,R., Usmani,K., Walker,D., White,C., Williams,A., Woodworth,J., Wright,R., Young,S., Yun,X., Han,Y., Kovar,C., Reid,J.G., Weinstock,G., Doddapaneni,H., Muzny,D.M., Worley,K.C. and Gibbs,R.A. https://www.ncbi.nlm.nih.gov/nuccore/ABRQ00000000.

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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© 2018-2019 by the Aiden Lab.