Dromedary (Camelus dromedarius)
The dromedary camels are the ones with only one hump. They can drink 30 gallons of water in 15 minutes! Read more about dromedaries on Wikipedia.
Photo by JamesDeMers from Pixabay [CC0 Creative Commons]
Chromosome-length genome assembly
Download the PRJNA234474_Ca_dromedarius_V1.0_HiC.fasta.gz file containing the chromosome-length (2n=74) assembly of the dromedary genome. All modifications with respect to the draft (see below) are annotated in the PRJNA234474_Ca_dromedarius_V1.0_HiC.assembly file. Some basic stats associated with the new reference, PRJNA234474_Ca_dromedarius_V1.0_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
1,981,467,617 | 105,614 | 69,067 | 747,808 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,004,792,918 | 31,314 | 72,916,538 | 122,183,487 |
Draft
The chromosome-length genome assembly is based on the draft assembly PRJNA234474_Ca_dromedarius_V1.0 (GCF_000767585.1), credited below.
Wu, Huiguang, Xuanmin Guang, Mohamed B. Al-Fageeh, Junwei Cao, Shengkai Pan, Huanmin Zhou, Li Zhang, et al. 2014. "Camelid Genomes Reveal Evolution and Adaptation to Desert Environments." Nature Communications 5 (October): 5188. https://doi.org/10.1038/ncomms6188.
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 muscle sample for in situ Hi-C preparation was obtained from Exotic Meat Market.
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).
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.
Wu, Huiguang, Xuanmin Guang, Mohamed B. Al-Fageeh, Junwei Cao, Shengkai Pan, Huanmin Zhou, Li Zhang, et al. 2014. "Camelid Genomes Reveal Evolution and Adaptation to Desert Environments." Nature Communications 5 (October): 5188. https://doi.org/10.1038/ncomms6188.
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.