Yellow-throated marten (Martes flavigula)

The yellow-throated marten appears to be much more advanced socially than their loner relatives. Some markings on their cotes almost definitely serve the purpose of biocommunication: the contrasting black head and white chin, bright yellow chest, and long, black tail are amazingly similar to patterns seen in highly social simians, such as squirrel monkeys! Read more about yellow-throated martens on Animal Diversity Web.

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Martes flavigula, yellow-throated marten by Rushen, [CC BY-SA 2.0], via flickr.com

Chromosome-length genome assembly

Download the mfla.min_150.pseudohap2.1_HiC.fasta.gz file containing the chromosome-length (2n=40) assembly of the yellow-throated marten genome. All modifications with respect to the draft (see below) are annotated in the mfla.min_150.pseudohap2.1_HiC.assembly file. Some basic stats associated with the new reference, mfla.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)
2,449,142,006
110,542
142,775
1,063,215
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,475,163,136
77,737
135,435,256
214,022,600
Draft

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

This genome assembly was created in collaboration with DNA Zoo Novosibirsk team. We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli and Dr. Alexander Graphodatsky for organizing this sequencing and bringing all of the collaborators together. Also we thank Olga Shilo (deputee director), Rosa Solovyova (head of carnivore department) and Svetlana Verkholantseva (veterinarian) from Rostislav Shilo Novosibirsk Zoo (Russia, Novosibirsk) who provided samples for a cell line. Samples were collected postmortem from a 15-year old male individual called Dixi. These cells were used for both DNA extraction for linked read sequencing and for the Hi-C experiment. DNA extraction and Zoo-FISH experiments were performed by Natalia Serdyukova and Dr. Violetta Beklemisheva. The draft assembly was performed by Sergei Kliver.

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 named Dixi, and obtained from Olga Shilo (deputee director), Rosa Solovyova (head of carnivore department) and Svetlana Verkholantseva (veterinarian) at the Rostislav Shilo Novosibirsk Zoo (Russia, Novosibirsk), provided to the Animal Cytogenetics Laboratory at the Institute of Molecular and Cellular Biology, Novosibirsk, Russia (Dr. Alexander Graphodatsky).

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 created in collaboration with DNA Zoo Novosibirsk team. We thank Dr. Rogell Powell (North Carolina State University) for funding 10x Genomics linked-read sequencing for the draft assembly and Dr. Klaus Koepfli and Dr. Alexander Graphodatsky for organizing this sequencing and bringing all of the collaborators together. Also we thank Olga Shilo (deputee director), Rosa Solovyova (head of carnivore department) and Svetlana Verkholantseva (veterinarian) from Rostislav Shilo Novosibirsk Zoo (Russia, Novosibirsk) who provided samples for a cell line. Samples were collected postmortem from a 15-year old male individual called Dixi. These cells were used for both DNA extraction for linked read sequencing and for the Hi-C experiment. DNA extraction and Zoo-FISH experiments were performed by Natalia Serdyukova and Dr. Violetta Beklemisheva. The draft assembly was performed by Sergei Kliver.

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.