Oncopeltus fasciatus genome annotations v0.5.3

<p>The <em>Oncopeltus fasciatus</em> genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. 
The <em>O. fasciatus</em> research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1.</p>
<p><em>Oncopeltus fasciatus</em> 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.</p>
<p>For example, this species has the same piercing and sucking type mouthparts as its less benign relatives, including the blood-sucking kissing bug, <em>Rhodnius prolixus</em>, and the brown marmorated stink bug, <em>Halyomorpha halys</em>, which are disease vector and agricultural pest species, respectively. Unlike the pest species, the benign, seed-feeding <em>Oncopeltus</em> can be functionally investigated in the lab by RNA interference (RNAi). Comparing the genomes, and conducting experimental lab work in <em>Oncopeltus</em>, will help to identify unique features of the pest species, and thus inform management strategies for them.</p>
<p>More generally, <em>Oncopeltus</em> 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.</p>
<p>This dataset presents the <em>Oncopeltus fasciatus</em> gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Oncopeltus fasciatus genome assembly 1.0. Further annotation method details will be available in a forthcoming publication.</p>
<p>NOTE: This gene set is an unstable pre-release (v0.5.3), and was provided to facilitate manual curation and analyses before the official gene set is released. Gene identifiers from this gene set will likely not be maintained.</p>
<p>If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: <a href="https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use">https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use</a></p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Oncopeltus fasciatus genome annotations v0.5.3 for genome assembly Oncopeltus fasciatus v1.0.</p> <p>File Name: oncfas_BCM_version_0.5.3.tar__0.gz</p><p>Resource Description: </p><p>The attached tar.gz archive (oncfas_BCM_version_0.5.3.tar_.gz) contains the following folders:</p>

<p>BCM_version_0.5.3.  This folder contains evidence files in gff3 format underlying the final gene predictions.</p>

<p>BCM_version_0.5.3/consensus_gene_set. This folder contains the following files:</p>

<p>OFAS.CDS.fna.gz. CDS sequences of <em>Oncopeltus fasciatus</em> genome annotations v0.5.3.</p>

<p>OFAS.faa.gz Amino acid sequences of <em>Oncopeltus fasciatus</em> genome annotations v0.5.3.</p>

<p>OFAS.fna.gz cDNA sequences of <em>Oncopeltus fasciatus</em> genome annotations v0.5.3.</p>

<p>OFAS.Models.gff3.gz Gff3 of all gene predictions of <em>Oncopeltus fasciatus</em> genome annotations v0.5.3.</p>

<p>OFAS.Models-NALmod.gff3.gz Gff3 of all gene predictions of <em>Oncopeltus fasciatus</em> genome annotations v0.5.3, modified by the National Agricultural Library to be compliant with gff3 specifications.</p>
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Tags: ars, data-gov, i5k, insects, milkweed-bug
Organization: Department of Agriculture