Acropora millepora stony coral (Acropora millepora)

Corals can reproduce asexually through fragmentation. Acropora millepora have some of the smallest fragments in their genus, under 6cm, that can survive at least 17 months! Read more about acropora millepora stony corals on Animal Diversity Web.

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Acropora millepora (Pink Coral), photo by Arthur Chapman [CC BY-NC 2.0], via flickr.com

Chromosome-length genome assembly

Download the amil_sf_1.1_HiC.fasta.gz file containing the chromosome-length (2n=28) assembly of the acropora millepora stony coral genome. All modifications with respect to the draft (see below) are annotated in the amil_sf_1.1_HiC.assembly file. Some basic stats associated with the new reference, amil_sf_1.1_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
349,002,992
35,631
19,473
180,633
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
387,097,822
2,649
22,621,383
30,199,759
Draft

The chromosome-length genome assembly is based on the draft assembly amil_sf_1.1 (GCF_004143615.1), credited below.

Ying, H., Hayward, D.C., Cooke, I., Wang, W., Moya, A., Siemering, K.R., Sprungala, S., Ball, E.E., Forêt, S., Miller, D.J., 2019. The Whole-Genome Sequence of the Coral Acropora millepora. Genome Biol. Evol. 11, 1374-1379. https://doi.org/10.1093/gbe/evz077.

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 branch sample for in situ Hi-C preparation was obtained from Alexander Haddad.

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.

Ying, H., Hayward, D.C., Cooke, I., Wang, W., Moya, A., Siemering, K.R., Sprungala, S., Ball, E.E., Forêt, S., Miller, D.J., 2019. The Whole-Genome Sequence of the Coral Acropora millepora. Genome Biol. Evol. 11, 1374-1379. https://doi.org/10.1093/gbe/evz077.

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.