Sable (Martes zibellina)

The sable has an unsually long gestation for a weasel, lasting up to 300 days due to their ability to delay the implantation of a fertilized egg in the uterine wall. Read more about sables on Britannica's website.

africa-animal-big-cat-88234.jpg

Sable marten by Е.Медведева, [CC BY-SA 3.0], via Wikimedia Commons

Chromosome-length genome assembly

Download the mzib.min_150.pseudohap2.1_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the sable genome. All modifications with respect to the draft (see below) are annotated in the mzib.min_150.pseudohap2.1_HiC.assembly file. Some basic stats associated with the new reference, mzib.min_150.pseudohap2.1_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,381,246,078
49,507
326,288
2,720,652
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,406,319,238
33,269
143,641,668
216,772,412
Draft

The chromosome-length genome assembly is based on the draft assembly mzib.min_150.pseudohap2.1, credited below.

This work was performed with funding from Dr. Rogell Powell (North Carolina State University) for 10x Genomics linked-read sequencing for the draft assembly. Dr. Klaus Koepfli (Smithsonian-Mason School of Conservation) and Dr. Alexander Graphodatsky (Institute of Molecular and Cellular Biology, Russia; IMCB) organized and brought all of the collaborators together to achieve chromosome-length genome assembly for the sable. Samples from male M. zibellina were provided by Tatiana Bulyonkova. The fibroblast cell line was established by Dr. Polina Perelman (IMCB). Cultured cells (passage 3) were used for both DNA extraction for linked read sequencing and for Hi-C experiments (passage 9). High-molecular weight DNA was extracted by Natalia Serdyukova (IMCB). Zoo-FISH experiments were performed by Dr. Violetta Beklemisheva (IMCB). The initial assembly was performed by Sergei Kliver (IMCB). Hi-C experiments and scaffolding to chromosomes were done by Ruqayya Khan, David Weisz and Olga Dudchenko. The genome annotation and a paper describing this research is in progress. IMCB work was supported by RFBR grant № 20-04-00808 and grants to A.S. Graphodatsky: RSF 19-14-00034 and Program of fundamental research of state academies of sciences 0246-2021-0015.

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 primary fibroblast sample for in situ Hi-C preparation was donated by a female individual, and obtained from Polina Perelman.

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 work was performed with funding from Dr. Rogell Powell (North Carolina State University) for 10x Genomics linked-read sequencing for the draft assembly. Dr. Klaus Koepfli (Smithsonian-Mason School of Conservation) and Dr. Alexander Graphodatsky (Institute of Molecular and Cellular Biology, Russia; IMCB) organized and brought all of the collaborators together to achieve chromosome-length genome assembly for the sable. Samples from male M. zibellina were provided by Tatiana Bulyonkova. The fibroblast cell line was established by Dr. Polina Perelman (IMCB). Cultured cells (passage 3) were used for both DNA extraction for linked read sequencing and for Hi-C experiments (passage 9). High-molecular weight DNA was extracted by Natalia Serdyukova (IMCB). Zoo-FISH experiments were performed by Dr. Violetta Beklemisheva (IMCB). The initial assembly was performed by Sergei Kliver (IMCB). Hi-C experiments and scaffolding to chromosomes were done by Ruqayya Khan, David Weisz and Olga Dudchenko. The genome annotation and a paper describing this research is in progress. IMCB work was supported by RFBR grant № 20-04-00808 and grants to A.S. Graphodatsky: RSF 19-14-00034 and Program of fundamental research of state academies of sciences 0246-2021-0015.

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.