Gemsbok cucumber (Citrullus naudinianus)

Citrullus naudinianus is a distant watermelon relative, native to southern Africa including Botswana, Namibia, Mozambique, Zambia, Zimbabwe and South Africa. Unlike all other watermelons, C. naudinianus has separate male and female plants! Read more about gemsbok cucumbers on Wikipedia.

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Immature fruit of Citrullus naudinianus, photo by Robert Jarret, USDA [CC]

Chromosome-length genome assembly

Download the CnF.asm.bp.p_ctg_HiC.fasta.gz file containing the chromosome-length (2n=22) assembly of the gemsbok cucumber genome. All modifications with respect to the draft (see below) are annotated in the CnF.asm.bp.p_ctg_HiC.assembly file. Some basic stats associated with the new reference, CnF.asm.bp.p_ctg_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
491,737,979
3,501
31,177,102
38,670,485
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
491,739,479
3,498
31,914,203
38,670,485
Draft

The chromosome-length genome assembly is based on the draft assembly CnF.asm.bp.p_ctg, credited below.

The draft assembly was generated by the DNA Zoo team using hifiasm (Cheng et al. 2021) from HiFi Pacific Biosciences data generated with support from the USDA Agricultural Research Service.

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 leaf sample for in situ Hi-C preparation was obtained from Robert Jarret (USDA).

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.

The draft assembly was generated by the DNA Zoo team using hifiasm (Cheng et al. 2021) from HiFi Pacific Biosciences data generated with support from the USDA Agricultural Research Service.

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.