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Hoary bat (Aeorestes cinereus)

Fondly referred to by some of the scientists chasing them around North America as "sky lions", hoary bats are the among the biggest, flashiest, and widest ranging bats on the continent! Read more about hoary bats on Bat Conservation International website.


Hoary Bat (Lasiurus cinereous). Photo by Paul Cryan

Chromosome-length genome assembly

Download the L.cinereus_Cryan_1219_p1.0_HiC.fasta.gz file containing the chromosome-length (2n=28) assembly of the hoary bat genome. All modifications with respect to the draft (see below) are annotated in the L.cinereus_Cryan_1219_p1.0_HiC.assembly file. Some basic stats associated with the new reference, L.cinereus_Cryan_1219_p1.0_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)

The chromosome-length genome assembly is based on the draft assembly L.cinereus_Cryan_1219_p1.0 (GCA_011751065.1), credited below.

Cornman, R., Cryan, P., Fike, J. and Oyler-Mccance, S. "Effective population size in the hoary bat." Unpublished.


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 left pectoral muscle sample for in situ Hi-C preparation was donated by a female individual, and obtained from Paul Cryan, USGS Fort Collins Science Center under Colorado Parks and Wildlife Scientific Collection License 19TR2010 from a recently deceased bat provided by Larmier County Public Health Department.

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).


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.

Cornman, R., Cryan, P., Fike, J. and Oyler-Mccance, S. "Effective population size in the hoary bat." Unpublished.

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.

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.


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 or leave a comment on the Forum.

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