Pine marten (Martes martes)
A group of pine martens is known as a "richness". This name likely came from the monetary value of their pelts in the European fur trade. Read more about pine martens on Animalia's website.
Pine Marten by Caroline Legg, [CC BY 2.0], via flickr.com
Chromosome-length genome assembly
Download the mmar.min_150.pseudohap2.1_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the pine marten genome. All modifications with respect to the draft (see below) are annotated in the mmar.min_150.pseudohap2.1_HiC.assembly file. Some basic stats associated with the new reference, mmar.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) |
---|---|---|---|
2,400,106,738 | 52,557 | 327,623 | 2,830,302 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
---|---|---|---|
2,425,306,698 | 36,351 | 144,638,580 | 216,853,607 |
Draft
The chromosome-length genome assembly is based on the draft assembly mmar.min_150.pseudohap2.1, credited below.
The draft assembly was created by Sergei Kliver (DNA Zoo Novosibirsk, Institute of Molecular and Cellular Biology) using 10X Genomic link-read sequencing data from high-molecular weight DNA extracted by Natalia Serdyukova (Institute of Molecular and Cellular Biology, Novosibirsk, Russia) from a cell line provided by Kunming Cell Bank of the Chinese Academy of Sciences, Kunming, Yunnan, China, through Drs. Malcolm Ferguson-Smith and Fengtang Yang at Department of Veterinary Medicine, University of Cambridge, UK to Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky). The collaboration with DNA Zoo was initiated with the help of Dr. Klaus Koepfli (Smithsonian Mason School of Conservation), and funding for the draft sequencing was provided by Dr. Roger Powell (North Carolina State University).
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 fibroblasts sample for in situ Hi-C preparation was donated by a male individual, and obtained from Kunming Cell Bank of the Chinese Academy of Sciences, Kunming, Yunnan, China, through Drs. Malcolm Ferguson-Smith and Fengtang Yang at Department of Veterinary Medicine, University of Cambridge, UK to Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky), provided to the DNA Zoo by Dr. 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.
The draft assembly was created by Sergei Kliver (DNA Zoo Novosibirsk, Institute of Molecular and Cellular Biology) using 10X Genomic link-read sequencing data from high-molecular weight DNA extracted by Natalia Serdyukova (Institute of Molecular and Cellular Biology, Novosibirsk, Russia) from a cell line provided by Kunming Cell Bank of the Chinese Academy of Sciences, Kunming, Yunnan, China, through Drs. Malcolm Ferguson-Smith and Fengtang Yang at Department of Veterinary Medicine, University of Cambridge, UK to Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky). The collaboration with DNA Zoo was initiated with the help of Dr. Klaus Koepfli (Smithsonian Mason School of Conservation), and funding for the draft sequencing was provided by Dr. Roger Powell (North Carolina State University).
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.