Fringe-lipped bat (Trachops cirrhosus)

The fringe-lipped bat is named for the wart-like bumps on their nose and lips. Read more about fringe-lipped bats on Bat Conservation International's website.

africa-animal-big-cat-88234.jpg

Photo of Trachops cirrhosus in Belize by Sherri and Brock Fenton

Chromosome-length genome assembly

Download the Trachops_cirrhosus_HiC.fasta.gz file containing the chromosome-length (2n=30) assembly of the fringe-lipped bat genome. All modifications with respect to the draft (see below) are annotated in the Trachops_cirrhosus_HiC.assembly file. Some basic stats associated with the new reference, Trachops_cirrhosus_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
2,164,629,387
432,771
60,077
743,085
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
2,179,538,887
396,524
124,458,213
194,552,972
Draft

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

The draft assembly was generated by the DNA Zoo team from short insert-size PCR-free DNA-Seq data using w2rap-contigger (Clavijo et al. 2017), see (Dudchenko et al., 2018) for details. The liver sample used for in situ Hi-C preparation (AMNH-AMCC-225240) came from a male individual of Trachops cirrhosis collected on the 26th of April, 2017 at the Ka'Kabish Archaeological Reserve in Orange Walk District, Belize (17.81531 N, 88.73057 W). Capture and export of this specimen were licensed under Belize Forest Department permits WL/2/1/17(16), WL/2/1/17(19), and WL/2/7/17(21). The voucher specimen and data for this sample are archived at the American Museum of Natural History under catalog number AMNH-Mammalogy-279525. We graciously thank Nancy Simmons (AMNH Department of Mammalogy), Svetlana Katanova (AMNH Ambrose Monell Cryo Collection), and Daniel Becker (University of Oklahoma) for access to this sample.

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 liver sample for in situ Hi-C preparation was donated by a male individual named 225240 (BPO 010), and obtained from the American Museum of Natural History under catalog number AMNH-Mammalogy-279525.

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.

The draft assembly was generated by the DNA Zoo team from short insert-size PCR-free DNA-Seq data using w2rap-contigger (Clavijo et al. 2017), see (Dudchenko et al., 2018) for details. The liver sample used for in situ Hi-C preparation (AMNH-AMCC-225240) came from a male individual of Trachops cirrhosis collected on the 26th of April, 2017 at the Ka'Kabish Archaeological Reserve in Orange Walk District, Belize (17.81531 N, 88.73057 W). Capture and export of this specimen were licensed under Belize Forest Department permits WL/2/1/17(16), WL/2/1/17(19), and WL/2/7/17(21). The voucher specimen and data for this sample are archived at the American Museum of Natural History under catalog number AMNH-Mammalogy-279525. We graciously thank Nancy Simmons (AMNH Department of Mammalogy), Svetlana Katanova (AMNH Ambrose Monell Cryo Collection), and Daniel Becker (University of Oklahoma) for access to this sample.

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.