American grasshopper (Schistocerca americana)
The American grasshopper can cause injury to citrus, corn, cotton, oats, peanuts, rye, sugarcane, tobacco, and vegetables. The species receives attention in Florida due to its defoliation of young citrus trees. The plants are damaged by the grasshopper gnawing on the leaves, and young vegetable plants can be eaten to the ground. Read more about American grasshoppers on University of Florida Extension website.
Schistocerca americana, photo by Brandon Woo (Hojun Song lab, Texas A&M)
Chromosome-length genome assembly
Download the iqSchAmer2.1.fasta.gz file containing the chromosome-length (2n=24) assembly of the American grasshopper genome. All modifications with respect to the draft (see below) are annotated in the iqSchAmer2.1.assembly file. Some basic stats associated with the new reference, iqSchAmer2.1, are listed below. The full data release can be explored here.
Contig length (bp) | Number of contigs | Contig N50 (bp) | Longest contig (bp) |
|---|---|---|---|
8,990,121,306 | 2,249 | 49,627,568 | 182,582,438 |
Scaffold length (bp) | Number of scaffolds | Scaffold N50 (bp) | Longest scaffold (bp) |
|---|---|---|---|
8,990,369,808 | 1,751 | 854,857,182 | 1,268,505,426 |
Draft
The chromosome-length genome assembly is based on the draft assembly Schistocerca_americana.12c.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 12 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 iqSchAmer2 (SAMN18214781), 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 12 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.
