Pacific pocket mouse (Perognathus longimembris pacificus)

The Pacific pocket mouse is tiny, weighing about the same as three pennies (6-7 grams)! This species was thought to be extinct until three small populations were discovered in 1993. Read more about Pacific pocket mice on the San Diego Zoo's website.

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Pacific pocket mouse peeking out of a pipe. Photo credit: San Diego Zoo

Chromosome-length genome assembly

Download the PPM_HiRise_rh_HiC.fasta.gz file containing the chromosome-length (2n=58) assembly of the Pacific pocket mouse genome. All modifications with respect to the draft (see below) are annotated in the PPM_HiRise_rh_HiC.assembly file. Some basic stats associated with the new reference, PPM_HiRise_rh_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,211,301,696
7,987
7,389,774
36,783,186
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,212,099,196
6,180
72,679,016
163,161,067
Draft

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

The draft genome assembly was created in collaboration between Dovetail Genomics and San Diego Zoo Global, using data from a fibroblast cell line banked by the San Diego Zoo in their Frozen Zoo.

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 primary fibroblasts sample for in situ Hi-C preparation was donated by a male individual, and obtained from Aryn Wilder, Frozen Zoo at San Diego Zoo.

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.

The draft genome assembly was created in collaboration between Dovetail Genomics and San Diego Zoo Global, using data from a fibroblast cell line banked by the San Diego Zoo in their Frozen Zoo.

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.