Pig-nosed turtle (Carettochelys insculpta)

The pig-nosed turtle is the only living member of its genus and does not have any known subspecies. Pig-nosed turtles are the only freshwater turtles that have flippers! Read more about pig-nosed turtles on Animalia website.

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"Pig-nose turtle" by wilth is licensed with CC BY-NC-SA 2.0. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/2.0/

Chromosome-length genome assembly

Download the Carettochelys_insculpta-1.0_HiC.fasta.gz file containing the chromosome-length (2n=34) assembly of the pig-nosed turtle genome. All modifications with respect to the draft (see below) are annotated in the Carettochelys_insculpta-1.0_HiC.assembly file. Some basic stats associated with the new reference, Carettochelys_insculpta-1.0_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,283,294,457
85,674
116,022
956,581
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,338,308,984
49,492
125,088,908
376,794,681
Draft

The chromosome-length genome assembly is based on the draft assembly Carettochelys_insculpta-1.0 (GCA_007922185.1), credited below.

Shaffer, H.B. and Minx, P., "The Carettochelys insculpta whole genome shotgun (WGS) project." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/VOCQ00000000.1.

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 pancreas sample for in situ Hi-C preparation was donated by a male individual named Warradjan, and obtained from Matthew Young & Arthur Georges (University of Canberra).

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). (Please note that the interactive figures are scaled 1:2.) 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.

Shaffer, H.B. and Minx, P., "The Carettochelys insculpta whole genome shotgun (WGS) project." Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/VOCQ00000000.1.

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.