Southern giant pouched rat (Cricetomys ansorgei)

In 2020, a Southern giant pouched rat named Magawa became the first rodent to be awarded the PDSA Gold medal for animal bravery! Read more about southern giant pouched rats on PDSA website.

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Photo of Southern giant pouched rat by Ehren Bentz

Chromosome-length genome assembly

Download the Cricetomys_ansorgei_HiC.fasta.gz file containing the chromosome-length (2n=80) assembly of the southern giant pouched rat genome. All modifications with respect to the draft (see below) are annotated in the Cricetomys_ansorgei_HiC.assembly file. Some basic stats associated with the new reference, Cricetomys_ansorgei_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,453,234,649
4,739
13,581,387
82,679,815
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,453,730,532
3,745
49,543,905
122,042,860
Draft

The chromosome-length genome assembly is based on the draft assembly 3745_assembly, credited below.

This genome assembly was produced by Dr. Ehren Bentz and Dr. Alexander Ophir in the Psychology department at Cornell University in collaboration with DNA Zoo. Whole genome sequencing was performed by the University of Georgia Genomics and Bioinformatics Core using Pacific Biosciences continuous long read sequencing. Reads were error corrected and assembled using Canu (Koren et al., 2017), and contigs were anchored to scaffolds using in situ Hi-C sequencing (Rao, Huntley et al., 2014), 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). The resulting chromosome-length scaffolds were then polished with PacBio long reads using Racon (Vaser, Sović et al., 2017).

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 liver sample for in situ Hi-C preparation was donated by a male individual named M1510886, and obtained from Ehren James Bentz, Ophir Lab (Cornell University).

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.

This genome assembly was produced by Dr. Ehren Bentz and Dr. Alexander Ophir in the Psychology department at Cornell University in collaboration with DNA Zoo. Whole genome sequencing was performed by the University of Georgia Genomics and Bioinformatics Core using Pacific Biosciences continuous long read sequencing. Reads were error corrected and assembled using Canu (Koren et al., 2017), and contigs were anchored to scaffolds using in situ Hi-C sequencing (Rao, Huntley et al., 2014), 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). The resulting chromosome-length scaffolds were then polished with PacBio long reads using Racon (Vaser, Sović et al., 2017).

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.