Dingo, Alpine ecotype (Canis lupus dingo, Alpine ecotype)
There are at least two dingo forms, we call ecotypes, that may have colonised Australia independently or may have diverged upon arrival in Australia. These ecotypes are most commonly called Desert and Alpine types. Read more about dingo, alpine ecotype on UNSW website.
Cooinda and Typia; Photo: Bargo Dingo Sanctuary
Chromosome-length genome assembly
Download the Cooinda_HYBRID_SCAFFOLD_NCBI_Nresized_merged_NOT_SCAFFOLDED_HiC.fasta.gz file containing the chromosome-length (2n=78) assembly of the dingo, alpine ecotype genome. All modifications with respect to the draft (see below) are annotated in the Cooinda_HYBRID_SCAFFOLD_NCBI_Nresized_merged_NOT_SCAFFOLDED_HiC.assembly file. Some basic stats associated with the new reference, Cooinda_HYBRID_SCAFFOLD_NCBI_Nresized_merged_NOT_SCAFFOLDED_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,409,754,062 | 1,960 | 10,905,882 | 45,123,703 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,422,245,913 | 1,342 | 64,624,203 | 125,073,439 |
Draft
The chromosome-length genome assembly is based on the draft assembly Cooinda_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. This page describes the Hi-C scaffolding of the original PacBio + BioNano draft. The post-Hi-C assembly was gap-filled & polished, and is now available on NCBI as UNSW_AlpineDingo_1.0.
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 female individual named Cooinda, and obtained from Vineyard Veterinary Hospital, Australia (coordinated by Robert Zammit and William Ballard).
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. This page describes the Hi-C scaffolding of the original PacBio + BioNano draft. The post-Hi-C assembly was gap-filled & polished, and is now available on NCBI as UNSW_AlpineDingo_1.0.
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.