Table of Contents
Oncopeltus fasciatus has been an established lab organism for over 60 years, and has been used for a wide range of studies from physiology to development and evolution. As a relatively conservative and generalized species, it affords a baseline against which other species can be compared.
For example, this species has the same piercing and sucking type mouthparts as its less benign relatives, including the blood-sucking kissing bug, Rhodnius prolixus, and the brown marmorated stink bug, Halyomorpha halys, which are disease vector and agricultural pest species, respectively. Unlike the pest species, the benign, seed-feeding Oncopeltus can be functionally investigated in the lab by RNA interference (RNAi). Comparing the genomes, and conducting experimental lab work in Oncopeltus, will help to identify unique features of the pest species, and thus inform management strategies for them.
More generally, Oncopeltus is a key species for comparisons across the insects. It is one of the few experimentally tractable hemimetabolous species that can ground comparisons with the completely metamorphosing species of the Holometabola (e.g., flies, beetles, wasps). Topics investigated in this framework include reproductive biology and development of the legs, wings, body segments, extraembryonic membranes, and overall establishment of the body plan.
Please cite one or more of the following publications when using the genome assembly Ofas_1.0, annotations BCMv0.5.3, or annotations OGSv1.1:
- Genome assembly Ofas_1.0, Genome annotations BCMv0.5.3, and Genome annotations OGSv1.1: Panfilio, K. A., Jentzsch, I. M. V., Benoit, J. B., Erezyilmaz, D., Suzuki, Y., Colella, S., ... & Weirauch, M. T. (2019). Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome biology, 20(1), 64.
- Genome assembly Ofas_1.0: (dataset) Murali, Shwetha C.; Bandaranaike, D.; Bellair, M.; et al. (2015). Oncopeltus fasciatus genome assembly 1.0. Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC/1173238
- Genome annotations BCMv0.5.3:(dataset) Hughes, D. S. T.; Koelzer, S.; Panfilio, K. A.; Richards, Stephen (2015). Oncopeltus fasciatus genome annotations v0.5.3. Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC/1173237
- Genome annotations OGSv1.1:(dataset) Vargas Jentzsch, Iris M.; Hughes, Daniel S. T.; Poelchau, Monica; et al. (2015). Oncopeltus fasciatus Official Gene set v1.1. Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC
- Analysis Name
- Whole genome assembly of Oncopeltus fasciatus
- Baylor College of Medicine genome assembly pipeline (NA)
- Oncopeltus fasciatus genome assembly 1.0
- Date performed
- Materials & Methods
Sequence generation for assembly. For this project we are generating fairly high coverage in a number of different insert sized libraries. The assembly strategy is based around a seed allpaths assembly (the Broad Allpaths assembler) followed by seed assembly improvement using homegrown tools, Atlas-link and Atlas-GapFill, which can significantly improve the results. Thus we generate sequence data to enable the Allpaths assembly. As of Nov 2011 this is: - 40X genome coverage in 180bp insert library (100bp reads forward and reverse); and 40X 3kb insert data. To enable better scaffolding and local gap filling we additionally generate 500bp, 1kb, 2kb, and 8kb insert sizes at > 20X coverage.
Publication status: Published, please cite https://doi.org/10.1186/s13059-019-1660-0 and https://doi.org/10.15482/USDA.ADC/1173238Source: Baylor College of Medicine i5K Project Summary
- Contig N50
- Scaffold N50
- GC Content