Dama gazelle (Nanger dama)

The dama gazelle is the world's largest gazelle! There are three recognized subspecies of Nanber dama; this assembly is for the N. dama ruficollis subspecies. Read more about dama gazelles on Smithsonian Conservation Biology Institute website.

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Dama gazelle by Valerie, [CC BY-NC-ND 2.0], via flickr.com

Chromosome-length genome assembly

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

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,981,624,220
71,445
270,108
2,197,470
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
3,013,446,760
38,032
156,272,796
258,512,208
Draft

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

The draft contig-based assembly was produced with 10X Genomics linked-read sequencing and assembled using Supernova version 2.0. The genetic material used to generate the contig-based assembly and the Hi-C data for chromosome-length scaffolding was collected from a male addra gazelle belonging to an ex situ herd managed at the Smithsonian Conservation Biology Institute in Front Royal, Virginia, USA.

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 named Gazilla, and obtained from Budhan Pukazhenthi, Klaus-Peter Koepfli (Smithsonian Conservation Biology Institute). We thank Smithsonian Conservation Biology Institute 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.

The draft contig-based assembly was produced with 10X Genomics linked-read sequencing and assembled using Supernova version 2.0. The genetic material used to generate the contig-based assembly and the Hi-C data for chromosome-length scaffolding was collected from a male addra gazelle belonging to an ex situ herd managed at the Smithsonian Conservation Biology Institute in Front Royal, Virginia, USA.

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.