Margined sweat bee (Lasioglossum marginatum)

Lasioglossum marginatum forms perennial colonies lasting five or six years, with hundreds of workers; this species is the only halictine bee with perennial colonies! Read more about margined sweat bees on Wikipedia.

africa-animal-big-cat-88234.jpg

Gideon Pisanty (Gidip), CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons

Chromosome-length genome assembly

Download the LMAR_genome_v2.1.1.fasta.gz file containing the chromosome-length (2n=76) assembly of the margined sweat bee genome. All modifications with respect to the draft (see below) are annotated in the LMAR_genome_v2.1.1.assembly file. Some basic stats associated with the new reference, LMAR_genome_v2.1.1, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
302,419,704
16,796
230,054
3,318,175
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
302,926,204
12,547
7,692,625
20,544,363
Draft

The chromosome-length genome assembly is based on the draft assembly LMAR_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: KMT5L-C10, Legacy ID: LMARC10, 4-letter alias: LMAR, alt: Apo0097, 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.