German Shepherd Dog (Canis lupus familiaris, German Shepherd)
German Shepherds are known for their intelligence and strength, which makes them a perfect choice for police work. A German Shepherd named Inspector Rex is the star of an Austrian Police procedural drama program! Read more about German Shepherd Dogs on American Kennel Club website.
Nala, the German Shepherd Dog that donated blood for this genome assembly. Photo by Outdoor Action Photography
Chromosome-length genome assembly
Download the ASM864105v1.fasta.gz file containing the chromosome-length (2n=78) assembly of the German Shepherd Dog genome. All modifications with respect to the draft (see below) are annotated in the ASM864105v1.assembly file. Some basic stats associated with the new reference, ASM864105v1, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,401,146,892 | 887 | 14,817,807 | 54,938,524 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,407,291,559 | 429 | 64,346,267 | 126,700,074 |
Draft
The chromosome-length genome assembly is based on the draft assembly Nala_HYBRID_SCAFFOLD_NCBI_Nresized_merged_NOT_SCAFFOLDED, credited below.
This genome assembly was generated as part of a collaborative effort led by J. William O. Ballard, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia. For more details see: Matt A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva K.F. Chan, Andre E. Minoche, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Richard J. Edwards, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanovic, Martin Smith, Erez Lieberman Aiden, Timothy P.L. Smith, Robert A. Zammit, J. William O. Ballard "De novo genome assembly of German Shepherd Dog (Canis lupus familiaris)". Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/VSDE00000000.1/.
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 blood sample for in situ Hi-C preparation was donated by a male individual named Tydus, and obtained from Susan Garrison (Cornell Veterinary Biobank).
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 assembly was generated as part of a collaborative effort led by J. William O. Ballard, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia. For more details see: Matt A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva K.F. Chan, Andre E. Minoche, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Richard J. Edwards, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanovic, Martin Smith, Erez Lieberman Aiden, Timothy P.L. Smith, Robert A. Zammit, J. William O. Ballard "De novo genome assembly of German Shepherd Dog (Canis lupus familiaris)". Unpublished. https://www.ncbi.nlm.nih.gov/nuccore/VSDE00000000.1/.
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.