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Northern long-eared bat (Myotis septentrionalis)

Northern myotis aka Northern long-eared bat has a distinctive foraging strategy. Instead of catching pray in mid-air like many other bats, it often feeds in dense forests while stationed on a tree. This is called "gleaning"! Read more about northern long-eared bats on Wikipedia.

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Northern Long-eared Bat, by Brookhaven National Laboratory [CC BY-NC-ND 2.0], via flickr.com

Chromosome-length genome assembly

Download the myse_ont_racon_pilon_HiC.fasta.gz file containing the chromosome-length (2n=44) assembly of the northern long-eared bat genome. All modifications with respect to the draft (see below) are annotated in the myse_ont_racon_pilon_HiC.assembly file. Some basic stats associated with the new reference, myse_ont_racon_pilon_HiC, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
1,970,955,988
22,038
203,380
1,797,245
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
1,977,996,141
4,948
96,689,946
221,655,331
Draft

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

The draft genome assembly was created by Devon O'Rourke, Matt MacManes and Jeff Foster. Oxford Nanopore R9 flowcells were used to generate the initial raw data (5818511 total reads; 29116606101 total bases ; 8882 read length N50) from a single female adult specimen collected from Tisbury, MA. These data were then basecalled with Albacore, reads trimmed with Porechop, and assembled into contigs with Flye (17,268 contigs, 1,998,235,525 bp, N50 217932). Illumina 150 bp PE reads were used to polish the scaffolds using three rounds of Racon and one round of Pilon.

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 muscle sample for in situ Hi-C preparation was donated by a male individual, and obtained from Devon O'Rourke (Northern Arizona University) and Luanne Johnson (Biodiversity Works).

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.

The draft genome assembly was created by Devon O'Rourke, Matt MacManes and Jeff Foster. Oxford Nanopore R9 flowcells were used to generate the initial raw data (5818511 total reads; 29116606101 total bases ; 8882 read length N50) from a single female adult specimen collected from Tisbury, MA. These data were then basecalled with Albacore, reads trimmed with Porechop, and assembled into contigs with Flye (17,268 contigs, 1,998,235,525 bp, N50 217932). Illumina 150 bp PE reads were used to polish the scaffolds using three rounds of Racon and one round of Pilon.

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.

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