Oncopeltus fasciatus Official Gene set v1.1

The Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1.

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.

This dataset presents the Oncopeltus fasciatus Official Gene Set (OGS) v1.1. The OGS is an integration of automatic gene predictions from Maker (done by Dan Hughes at Baylor) with manual annotations by the research community (done via Web Apollo).

If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use

• Resource Title: Oncopeltus fasciatus Official Gene Set OGS_v1.1 for genome assembly Oncopeltus fasciatus v1.0.

  File Name: OFAS_OGS_v1_1.tar__0.gz

  Resource Description:

  Due to assembly limitations of this draft genome, some manually annotated gene models were split across scaffolds. Like complete gene models, each split part of a given gene has its own unique ID in the "original" data set, comprised of the gff file as well as fasta files for transcripts' cDNA (including any UTR: "cdna"), coding sequence nucleotides only ("cds"), and the protein translation ("pep"). In a second step, we manually stitched the split models together, creating one model per gene, and where the stitched model has its own unique ID. Since transcript stitching ignores scaffold coordinate positions, there is no gff, but there are all three flavors of fasta file (cdna, cds, pep) for the "merged" data set. The remaining files are documentation in support of the stitching. The Excel spreadsheet tracks which original models were replaced by which stitched versions. In total, 121 original, split models were stitched into 55 new models, with up to 5 original models corresponding to one stitched gene model. The "split-removed" files are the set of complete models only (121 split models removed), and the "stitched" files are the 55 manually fixed new models only. "Merged" is then just the concatenation of those two data sets.