Central American locust (Schistocerca piceifrons)

Schistocerca piceifrons is a swarming locust of tropical America closely related to non-swarming Schistocerca americana. Read more about Central American locusts on Wikipedia.

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Schistocerca piceifrons nymphs, photo by Hojun Song (Texas A&M)

Chromosome-length genome assembly

Download the iqSchPice1.1.fasta.gz file containing the chromosome-length (2n=24) assembly of the Central American locust genome. All modifications with respect to the draft (see below) are annotated in the iqSchPice1.1.assembly file. Some basic stats associated with the new reference, iqSchPice1.1, are listed below. The full data release can be explored here.

Contig length (bp)
Number of contigs
Contig N50 (bp)
Longest contig (bp)
8,741,999,389
3,416
27,424,730
165,995,124
Scaffold length (bp)
Number of scaffolds
Scaffold N50 (bp)
Longest scaffold (bp)
8,742,459,392
2,493
854,032,331
1,254,751,361
Draft

The chromosome-length genome assembly is based on the draft assembly Schistocerca_piceifrons.c14.filt.bp.p_ctg, credited below.

The draft genome assembly was generated by USDA-ARS team in Hilo, HI. Approximately 5 ug was used to create PacBio HiFi sequencing libraries using the SMRTbell Express Template Prep Kit 2.0 following standard low input DNA procedures and size selection to remove fragments shorter than 3kb using AMPure size selection. The resulting libraries were sequenced on a PacBio Sequel II system using 18 SMRT cell 8M runs to achieve greater than 20X coverage of the genome. Prior to assembly, raw HiFi reads were filtered using HiFiAdapterFilt to remove any CCS reads that contain PacBio adapter sequence. The filtered data was assembled using HiFiASM (v. 0.15.4) using default parameters in diploid mode. This genome assembly is part of the Behavioral Plascticity Research Institue (BPRI) effort.

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 hind femur sample for in situ Hi-C preparation was donated by a female individual named iqSchPice1 (SAMN18214782), and obtained from Hojun Song, Texas A&M 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.

The draft genome assembly was generated by USDA-ARS team in Hilo, HI. Approximately 5 ug was used to create PacBio HiFi sequencing libraries using the SMRTbell Express Template Prep Kit 2.0 following standard low input DNA procedures and size selection to remove fragments shorter than 3kb using AMPure size selection. The resulting libraries were sequenced on a PacBio Sequel II system using 18 SMRT cell 8M runs to achieve greater than 20X coverage of the genome. Prior to assembly, raw HiFi reads were filtered using HiFiAdapterFilt to remove any CCS reads that contain PacBio adapter sequence. The filtered data was assembled using HiFiASM (v. 0.15.4) using default parameters in diploid mode. This genome assembly is part of the Behavioral Plascticity Research Institue (BPRI) effort.

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.