California sea hare (Aplysia californica)
Sea hares, incluidng Aplysia californica, are popular model organisms in neuroscience. Aplysia has one of the earliest mentions in the literature of any animal, the first authentic description being by Pliny in his Historia Naturalis, c. 60 A.D.! Read more about California sea hares in Current Biology.
Sea Hare Dorsal Surface Aplysia californica, by Jerry Kirkhart [CC BY 2.0], from flickr.com
Chromosome-length genome assembly
Download the AplCal3.0_HiC.fasta.gz file containing the chromosome-length (n=17) assembly of the California sea hare genome. All modifications with respect to the draft (see below) are annotated in the AplCal3.0_HiC.assembly file. Some basic stats associated with the new reference, AplCal3.0_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
737,797,487 | 170,984 | 9,329 | 174,336 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
927,640,480 | 7,336 | 52,647,889 | 114,020,125 |
Draft
The chromosome-length genome assembly is based on the draft assembly AplCal3.0 (GCF_000002075.1), credited below.
Di Palma,F., Alfoldi,J., Johnson,J., Berlin,A., Gnerre,S., Jaffe,D., MacCallum,I., Young,S., Walker,B.J. and Lindblad-Toh,K. "The Draft Genome of Aplysia californica." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/AASC00000000.3.
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 Leonid Moroz, University of Florida. We thank Moroz for additional samples for this species.
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.
Di Palma,F., Alfoldi,J., Johnson,J., Berlin,A., Gnerre,S., Jaffe,D., MacCallum,I., Young,S., Walker,B.J. and Lindblad-Toh,K. "The Draft Genome of Aplysia californica." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/AASC00000000.3.
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.