Sea squirt (Ciona intestinalis/robusta)

Ciona intestinalis/robusta is a large solitary sea squirt which grows up to 15 cm in length. It is widely believed to be native to the northern Atlantic; however C. intestinalis is now a cosmopolitan species inhabiting sub-arctic, temperate and tropical waters! Read more about sea squirts on Invasite Species Compendium website.

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Credit: Doug McMinimy, Emma Farley, University of California, San Diego [CC]

Chromosome-length genome assembly

Download the Ciona_intestinalis_HT_Hoya_T-line_assembly_2019_HiC.fasta.gz file containing the chromosome-length (2n=28) assembly of the sea squirt genome. All modifications with respect to the draft (see below) are annotated in the Ciona_intestinalis_HT_Hoya_T-line_assembly_2019_HiC.assembly file. Some basic stats associated with the new reference, Ciona_intestinalis_HT_Hoya_T-line_assembly_2019_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
122,951,598
144
3,235,000
6,052,504
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
123,005,100
74
8,661,385
15,691,106
Draft

The chromosome-length genome assembly is based on the draft assembly Ciona_intestinalis_HT_Hoya_T-line_assembly_2019 (GCA_009617815.1), credited below.

Satou, Y., Nakamura, R., Yu, D., Yoshida, R., Hamada, M., Fujie, M., Hisata, K., Takeda, H., Satoh, N., 2019. A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. Genome Biol. Evol. 11, 3144-3157. https://doi.org/10.1093/gbe/evz228.

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 sample for in situ Hi-C preparation was obtained from Fabian Lim, Emma Farley (UCSD).

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.

Satou, Y., Nakamura, R., Yu, D., Yoshida, R., Hamada, M., Fujie, M., Hisata, K., Takeda, H., Satoh, N., 2019. A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. Genome Biol. Evol. 11, 3144-3157. https://doi.org/10.1093/gbe/evz228.

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.