Tree pangolin (Phataginus tricuspis)

The tree pangolin aka the white-bellied pangolin is one of eight extant species of pangolins ("scaly anteaters"), and is native to equatorial Africa. Like other pangolins, the tree pangolin does not have any teeth. Instead of teeth, it has a gizzard-like stomach full of stones and sand it ingests. Before entering water, the tree pangolin can also fill its stomach with air to aid in buoyancy for well-developed swimming! Read more about tree pangolins on National Geographic website.

Copyright: ehbidault, some rights reserved (CC-BY-NC), via inaturalist.org

Chromosome-length genome assembly

Download the Jaziri_pseudohap2_scaffolds_HiC.fasta.gz file containing the chromosome-length (2n=114) assembly of the tree pangolin genome. All modifications with respect to the draft (see below) are annotated in the Jaziri_pseudohap2_scaffolds_HiC.assembly file. Some basic stats associated with the new reference, Jaziri_pseudohap2_scaffolds_HiC, are listed below. The full data release can be explored here.

Draft

The chromosome-length genome assembly is based on the draft assembly Jaziri_pseudohap2_scaffolds, credited below.

Jaziri's assembly was made possible through a collaboration of the following individuals: Tom Smith, Department of Ecology and Evolutionary Biology and Director of the Center for Tropical Research at UCLA; Klaus-Peter Koepfli, Center for Species Survival, Smithsonian Conservation Biology Institute; Kenneth Kaemmerer, Curator of Mammals, and Ginger Sturgeon, Director of Animal Health, Pittsburgh Zoo & PPG Aquarium; Jan Janecka, Department of Biological Sciences, Duquesne University; and Olga Dudchenko, Arina Omer and Erez Aiden, The Center for Genome Architecture, Baylor College of Medicine and Rice 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 blood sample for in situ Hi-C preparation was donated by a female individual named Jaziri, and obtained from Pittsburgh Zoo & PPG Aquarium.

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.

Jaziri's assembly was made possible through a collaboration of the following individuals: Tom Smith, Department of Ecology and Evolutionary Biology and Director of the Center for Tropical Research at UCLA; Klaus-Peter Koepfli, Center for Species Survival, Smithsonian Conservation Biology Institute; Kenneth Kaemmerer, Curator of Mammals, and Ginger Sturgeon, Director of Animal Health, Pittsburgh Zoo & PPG Aquarium; Jan Janecka, Department of Biological Sciences, Duquesne University; and Olga Dudchenko, Arina Omer and Erez Aiden, The Center for Genome Architecture, Baylor College of Medicine and Rice 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 theaidenlab@gmail.com or leave a comment on the Forum.

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