Plains spotted skunk (Spilogale interrupta)

Spilogale interrupta is one of 4 newly-recognized species of spotted skunks in the United States. Read more about plains spotted skunks on SciTechDaily website.

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Plains spotted skunk, photo by Robert C. Dowler, Angelo State University [CC]

Chromosome-length genome assembly

Download the polished_2_HiC.fasta.gz file containing the chromosome-length (2n=64) assembly of the plains spotted skunk genome. All modifications with respect to the draft (see below) are annotated in the polished_2_HiC.assembly file. Some basic stats associated with the new reference, polished_2_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,367,126,711
1,092
16,288,691
66,102,683
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,367,379,711
586
84,003,853
147,353,149
Draft

The chromosome-length genome assembly is based on the draft assembly polished_2, credited below.

The draft genome for this assembly was generated from an ear punch collected from a male live captured near Polo, South Dakota, by Merav Ben-David, Robert Riotto, and Zachariah Bell from the University of Wyoming, and Samantha Fino from South Dakota State University (under permit SD_DGFP #35). The de novo assembly of the draft genome (including DNA extraction from the ear punch, construction of the long-insert DNA library, and sequencing on PacBio Sequel instrument) was performed by Maggie Weitzman and Douglas Turnbull from the University of Oregon Genomics and Cell Characterization Core Facility, and Vikram Chhatre from the University of Wyoming using high coverage PacBio sequences. DNA Zoo completed a Hi-C analyses to provide chromosome-level information using a sample provided by Robert Dowler from the Angelo State Natural History Collections. That sample of a male was obtained from a fur trapper (Gerald Herbst under permit 00034475). The animal was harvested near Chamberlain, South Dakota.

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 ear punch sample for in situ Hi-C preparation was donated by a male individual, and obtained from Robert Dowler (Angelo State Natural History Collections).

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 for this assembly was generated from an ear punch collected from a male live captured near Polo, South Dakota, by Merav Ben-David, Robert Riotto, and Zachariah Bell from the University of Wyoming, and Samantha Fino from South Dakota State University (under permit SD_DGFP #35). The de novo assembly of the draft genome (including DNA extraction from the ear punch, construction of the long-insert DNA library, and sequencing on PacBio Sequel instrument) was performed by Maggie Weitzman and Douglas Turnbull from the University of Oregon Genomics and Cell Characterization Core Facility, and Vikram Chhatre from the University of Wyoming using high coverage PacBio sequences. DNA Zoo completed a Hi-C analyses to provide chromosome-level information using a sample provided by Robert Dowler from the Angelo State Natural History Collections. That sample of a male was obtained from a fur trapper (Gerald Herbst under permit 00034475). The animal was harvested near Chamberlain, South Dakota.

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.