Chinese pangolin (Manis pentadactyla)
The word 'pangolin' comes from the Malay word 'penggulung' which means roller. Pangolins may roll into a ball when they feel threatened. Read more about chinese pangolins on the National Geographic's website.
Manis pentadactyla pentadactyla (2010.07.15), photo by Skink Chen [CC BY-NC-ND 2.0], via flickr.com
Chromosome-length genome assembly
Download the M_pentadactyla-1.1.1_HiC.fasta.gz file containing the chromosome-length (2n=40) assembly of the chinese pangolin genome. All modifications with respect to the draft (see below) are annotated in the M_pentadactyla-1.1.1_HiC.assembly file. Some basic stats associated with the new reference, M_pentadactyla-1.1.1_HiC, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
1,998,937,739 | 353,949 | 20,721 | 292,755 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
2,215,491,672 | 71,390 | 111,940,472 | 195,883,037 |
Draft
The chromosome-length genome assembly is based on the draft assembly M_pentadactyla-1.1.1 (GCA_000738955.1), 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 donated by a male individual, and 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. Jason S.C. Chin (Taipei Zoo), Dr. Melody Roelke (FNLCR, U.S.), and Dr. Warren Johnson (SI, U.S.). Acknowledgments to Dr. Carlos Driscoll, Dr. Christina Barr, Dr. David Goldman (NIAAA, U.S.), and Russ Hansen (NCI, 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 thednazoo@gmail.com or leave a comment on the Forum.