Golden hamster (Mesocricetus auratus)
Golden hamsters have the ability to quickly metabolize alcohol so that they can eat fermented fruit, their usual food during the winter months. This makes these hamsters great specimens for studies on alcohol! Read more about golden hamsters in Wikipedia.
Photo by Nana-ne from Pixabay
Chromosome-length genome assembly
Download the golden_hamster_wtdbg2.shortReadsPolished_HiC.fasta.gz file containing the chromosome-length (2n=44) assembly of the golden hamster genome. All modifications with respect to the draft (see below) are annotated in the golden_hamster_wtdbg2.shortReadsPolished_HiC.assembly file. Some basic stats associated with the new reference, golden_hamster_wtdbg2.shortReadsPolished_HiC, are listed below. The full data release can be explored here. Note that chromosome-length genome assembly based on another draft is available for this species, here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
2,413,904,466 | 11,512 | 1,999,004 | 9,998,914 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,415,569,966 | 8,181 | 109,859,428 | 150,942,546 |
Draft
The chromosome-length genome assembly is based on the draft assembly golden_hamster_wtdbg2.shortReadsPolished, credited below.
This genome assembly was generated in collaboration with Emanuel Wyler, Tatiana Borodina, Claudia Quedenau, Janine Altmüller and Markus Landthaler at Max Delbruck Center for Molecular Medicine, as well as Jakob Trimpert and Sandro Andreotti at Free University Berlin. The assembly is based on a long-read draft. Long-read sequencing was done by the MDC team with Oxford Nanopore (Promethion), with about 30x coverage and 50 kB median length of the sequences, polished with Illumina WGS data, also generated by MDC. The draft assembly was generated using wtdbg2 by the DNA Zoo team.
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, and provided to us by BioChemed Services.
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 in collaboration with Emanuel Wyler, Tatiana Borodina, Claudia Quedenau, Janine Altmüller and Markus Landthaler at Max Delbruck Center for Molecular Medicine, as well as Jakob Trimpert and Sandro Andreotti at Free University Berlin. The assembly is based on a long-read draft. Long-read sequencing was done by the MDC team with Oxford Nanopore (Promethion), with about 30x coverage and 50 kB median length of the sequences, polished with Illumina WGS data, also generated by MDC. The draft assembly was generated using wtdbg2 by the DNA Zoo team.
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.