Bicolored striped sweat bee (Agapostemon virescens)

Agapostemon virescens, the bicolored striped-sweat bee, is a species of sweat bee in the family Halictidae. It is found in North America Read more about bicolored striped sweat bees on iNaturalist.org.

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Photo 12194689, (c) Heather Holm, some rights reserved (CC BY-NC), via iNaturalist.org (https://www.inaturalist.org/photos/12194689)

Chromosome-length genome assembly

Download the AVIR_genome_v2.1.0.fasta.gz file containing the chromosome-length (2n=36) assembly of the bicolored striped sweat bee genome. All modifications with respect to the draft (see below) are annotated in the AVIR_genome_v2.1.0.assembly file. Some basic stats associated with the new reference, AVIR_genome_v2.1.0, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
429,412,550
80,958
13,733
232,240
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
470,107,380
52,668
17,608,045
25,019,036
Draft

The chromosome-length genome assembly is based on the draft assembly AVIR_genome_v1.0, credited below.

This genome assembly was created in collaboration with the Kocher Lab at Princeton University. The draft was assembled with Supernova assembler using 10x Genomics linked-read libraries. For details see https://www.biorxiv.org/content/10.1101/2021.04.14.439731v1..

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 head and thorax sample for in situ Hi-C preparation was donated by a female individual named COI-eq ID: BER7-C4, Legacy ID: BER7-C4, 4-letter alias: AVIR, alt: Apo0002, and obtained from Kocher Lab, Princeton University.

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.

This genome assembly was created in collaboration with the Kocher Lab at Princeton University. The draft was assembled with Supernova assembler using 10x Genomics linked-read libraries. For details see https://www.biorxiv.org/content/10.1101/2021.04.14.439731v1..

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.