Subterranean clover (Trifolium subterraneum)

The plant's name comes from its underground seed development, a characteristic not possessed by other clovers. Read more about subterranean clovers on Wikipedia.

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Photo Description - The Subterranean clover (Trifolium subterraneum) cv Daliak. Photo Credits and acknowledgements - Dr Parwinder Kaur [CC].

Chromosome-length genome assembly

Download the TrSub3.fasta.gz file containing the chromosome-length (2n=16) assembly of the subterranean clover genome. All modifications with respect to the draft (see below) are annotated in the TrSub3.assembly file. Some basic stats associated with the new reference, TrSub3, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
414,049,588
74,610
17,232
216,636
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
473,152,109
24,725
56,309,329
65,199,063
Draft

The chromosome-length genome assembly is based on the draft assembly TSUd_r1.1 (GCA_001742945.1), credited below.

Hirakawa, H., Kaur, P., Shirasawa, K., Nichols, P., Nagano, S., Appels, R., Erskine, W., Isobe, S.N., 2016. Draft genome sequence of subterranean clover, a reference for genus Trifolium. Sci. Rep. 6, 30358. https://doi.org/10.1038/srep30358.

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 leaves sample for in situ Hi-C preparation was obtained from Parwinder Kaur (University of Western Australia).

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.

Hirakawa, H., Kaur, P., Shirasawa, K., Nichols, P., Nagano, S., Appels, R., Erskine, W., Isobe, S.N., 2016. Draft genome sequence of subterranean clover, a reference for genus Trifolium. Sci. Rep. 6, 30358. https://doi.org/10.1038/srep30358.

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.