Indian flying fox (Pteropus giganteus)

The Indian flying fox is one of the largest bats in the world! They have a wingspan of 1.2-1.5 meters wide. Read more about Indian flying foxes on Animal Diversity's website.

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Indian Flying Fox by Sergey Yeliseev, [CC BY-NC-ND 2.0], via flickr.com

Chromosome-length genome assembly

Download the Ma_sr-lr_union100_HiC.fasta.gz file containing the chromosome-length (2n=38) assembly of the Indian flying fox genome. All modifications with respect to the draft (see below) are annotated in the Ma_sr-lr_union100_HiC.assembly file. Some basic stats associated with the new reference, Ma_sr-lr_union100_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
1,967,309,452
34,202
242,117
2,330,013
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
1,984,933,311
15,717
116,067,308
189,301,115
Draft

The chromosome-length genome assembly is based on the draft assembly Ma_sr-lr_union100 (GCA_902729225.1), credited below.

Fouret, J., Brunet, F.G., Binet, M., Aurine, N., Enchéry, F., Croze, S., Guinier, M., Goumaidi, A., Preininger, D., Volff, J.-N., Bailly-Bechet, M., Lachuer, J., Horvat, B., Legras-Lachuer, C., 2020. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front. Microbiol. 11, 1807. https://doi.org/10.3389/fmicb.2020.01807.

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 male individual, and obtained from Houston Zoo.

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). 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.

Fouret, J., Brunet, F.G., Binet, M., Aurine, N., Enchéry, F., Croze, S., Guinier, M., Goumaidi, A., Preininger, D., Volff, J.-N., Bailly-Bechet, M., Lachuer, J., Horvat, B., Legras-Lachuer, C., 2020. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front. Microbiol. 11, 1807. https://doi.org/10.3389/fmicb.2020.01807.

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.