Brown desert mouse (Pseudomys desertor)
The desert mouse has a high reproductive potential, even for the Pseudomys genus! With an oestrus cycle of seven to nine days, a mean litter size of three, a gestation period of 27-28 days, the desert mice populations can increase dramatically during mating seasons. Read more about brown desert mice on Atlas of Living Australia website.
Pseudomys desertor, the brown desert mouse. Source: Atlas of Living Australia / Photographer: Margarita Steinhardt
Chromosome-length genome assembly
Download the Pseudomys_desertor_wtdbg2_polished_HiC.fasta.gz file containing the chromosome-length (2n=48) assembly of the brown desert mouse genome. All modifications with respect to the draft (see below) are annotated in the Pseudomys_desertor_wtdbg2_polished_HiC.assembly file. Some basic stats associated with the new reference, Pseudomys_desertor_wtdbg2_polished_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,166,607,581 | 7,610 | 581,968 | 4,440,066 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,170,793,581 | 3,545 | 100,445,124 | 185,756,746 |
Draft
The chromosome-length genome assembly is based on the draft assembly Pseudomys_desertor_wtdbg2_polished, credited below.
This genome was done as part of a collaboration between DNA Zoo, Museums Victoria and Oz Mammal Genomics. The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using Oxford Nanopore reads polished with short-insert size Illumina reads.
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, and obtained from Kevin Rowe, Museums Victoria.
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.
This genome was done as part of a collaboration between DNA Zoo, Museums Victoria and Oz Mammal Genomics. The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using Oxford Nanopore reads polished with short-insert size Illumina reads.
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.