Sunda pangolin (Manis javanica)

Sunda pangolins are the most widely distributed pangolin species in Asia, ranging across much of Southeast Asia. As compared to Chinese pangolin, they have fewer rows of scales on their backs, longer tails, and shorter forelimb claws. They are also more likely to climb trees to reach ant nests, using their prehensile tails to cling to branches! Read more about sunda pangolins on National Geographic website.

Sunda pangolin, photo by budak [CC BY-NC-ND 2.0], via flickr.com

Chromosome-length genome assembly

Download the ManJav1.0_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the sunda pangolin genome. All modifications with respect to the draft (see below) are annotated in the ManJav1.0_HiC.assembly file. Some basic stats associated with the new reference, ManJav1.0_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly ManJav1.0 (GCF_001685135.1), credited below.

Choo, S.W., Rayko, M., Tan, T.K., Hari, R., Komissarov, A., Wee, W.Y., Yurchenko, A.A., Kliver, S., Tamazian, G., Antunes, A., Wilson, R.K., Warren, W.C., Koepfli, K.-P., Minx, P., Krasheninnikova, K., Kotze, A., Dalton, D.L., Vermaak, E., Paterson, I.C., Dobrynin, P., Sitam, F.T., Rovie-Ryan, J.J., Johnson, W.E., Yusoff, A.M., Luo, S.-J., Karuppannan, K.V., Fang, G., Zheng, D., Gerstein, M.B., Lipovich, L., O'Brien, S.J., Wong, G.J., 2016. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Res. 26, 1312-1322. https://doi.org/10.1101/gr.203521.115.

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 obtained from Dr. Polina Perelman (IMCB, Russia) who established them at the Laboratory of Genomic Diversity (Dr. Stephen O'Brien) from samples collected by Dr. Shujin Luo (Peking University, China), Dr. Norman Lim (NIE, Singapore), and Dr. Soon-Hock Oh (Singapore Zoo). Acknowledgments to Dr. Melody Roelke (FNLCR, U.S.), Dr. Carlos Driscoll, Dr. Christina Barr, Dr. David Goldman (NIAAA, U.S.), and Russ Hansen (NCI-Frederick, U.S.).

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.

Choo, S.W., Rayko, M., Tan, T.K., Hari, R., Komissarov, A., Wee, W.Y., Yurchenko, A.A., Kliver, S., Tamazian, G., Antunes, A., Wilson, R.K., Warren, W.C., Koepfli, K.-P., Minx, P., Krasheninnikova, K., Kotze, A., Dalton, D.L., Vermaak, E., Paterson, I.C., Dobrynin, P., Sitam, F.T., Rovie-Ryan, J.J., Johnson, W.E., Yusoff, A.M., Luo, S.-J., Karuppannan, K.V., Fang, G., Zheng, D., Gerstein, M.B., Lipovich, L., O'Brien, S.J., Wong, G.J., 2016. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Res. 26, 1312-1322. https://doi.org/10.1101/gr.203521.115.

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 theaidenlab@gmail.com or leave a comment on the Forum.

ARC-Logo-Final-2018-01.png

© 2018-2020 by the Aiden Lab.