Indian muntjac (Muntiacus muntjak)

The Indian muntjac is also called the southern red muntjac or barking deer. Muntjac's bark is quite the source of confusion: the groaning sound they make leads to the formation of many paranormal stories! Read more about Indian muntjacs on Animalia website.

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Indian muntjac, by Cloudtail the Snow Leopard [CC BY-NC-ND 2.0], via flickr.com

Chromosome-length genome assembly

Download the CMJ_HiC.fasta.gz file containing the chromosome-length (2n=6) assembly of the Indian muntjac genome. All modifications with respect to the draft (see below) are annotated in the CMJ_HiC.assembly file. Some basic stats associated with the new reference, CMJ_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,607,042,195
768,753
10,910
106,210
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,706,609,549
377,810
705,141,453
1,134,692,574
Draft

The chromosome-length genome assembly is based on the draft assembly CMJ (GCA_006409035.1), credited below.

Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, Chenzhou, Yin, Y., Wang, Yu, Zhao, Y., Zhang, Chen, Wang, Z., Qin, Y., Liu, W., Wang, B., Ren, Y., Zhang, R., Zeng, Y., Fonseca, R.R. da, Wei, B., Li, R., Wan, W., Zhao, R., Zhu, W., Wang, Yutao, Duan, S., Gao, Y., Zhang, Y.E., Chen, C., Hvilsom, C., Epps, C.W., Chemnick, L.G., Dong, Y., Mirarab, S., Siegismund, H.R., Ryder, O.A., Gilbert, M.T.P., Lewin, H.A., Zhang, G., Heller, R., Wang, W., 2019. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364, eaav6202. https://doi.org/10.1126/science.aav6202.

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 fibroblast-like immortal cell line sample for in situ Hi-C preparation was donated by a male individual, and obtained from Kazuhiro Maeshima, National Institute of Genetics, Japan.

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.

Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, Chenzhou, Yin, Y., Wang, Yu, Zhao, Y., Zhang, Chen, Wang, Z., Qin, Y., Liu, W., Wang, B., Ren, Y., Zhang, R., Zeng, Y., Fonseca, R.R. da, Wei, B., Li, R., Wan, W., Zhao, R., Zhu, W., Wang, Yutao, Duan, S., Gao, Y., Zhang, Y.E., Chen, C., Hvilsom, C., Epps, C.W., Chemnick, L.G., Dong, Y., Mirarab, S., Siegismund, H.R., Ryder, O.A., Gilbert, M.T.P., Lewin, H.A., Zhang, G., Heller, R., Wang, W., 2019. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364, eaav6202. https://doi.org/10.1126/science.aav6202.

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.