Leptinotarsa decemlineata Official Gene set v1.2
The Leptinotarsa decemlineata genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The L. decemlineata research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. OGSv1.1 is an integration of automatic gene predictions from Maker (performed by Dan Hughes at Baylor College of Medicine) with manual annotations by the research community (done via the Apollo manual annotation software). The coordinates of OGSv1.1 were converted to the latest genome assembly, GCF_000500325.1, using coordinates_conversion and remap-gff3, to generate OGSv1.2.
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
Resources in this dataset:Resource Title: Leptinotarsa decemlineata Official Gene Set OGSv1.2. File Name: lepdec_OGSv1-2.tar.gzResource Description: The attached tar.gz archive (lepdec_OGSv1-2.tar.gz) contains the following files:
* lepdec_OGSv1.2_GCF_000500325.1_cds.fa - CDS sequences for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1_pep.fa - protein sequences for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1_trans.fa - transcript sequences for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1.gff3 - GFF3 file for OGSv1.2
* lepdec_OGSv1.2_GCF_000500325.1_removed-features.tsv - a list of features removed between OGSv1.1 and OGSv1.2. The list includes feature type, ID, Name, and owner.
* lepdec_OGSv1.2_GCF_000500325.1_update-summary.tsv - summary statistics of the features removed between OGSv1.1 and OGSv1.2
Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[
"005:18"
]
|
| contactPoint |
{
"fn": "Schoville, Sean",
"hasEmail": "mailto:sean.schoville@wisc.edu"
}
|
| description | <p>The <em>Leptinotarsa decemlineata</em> genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The <em>L. decemlineata</em> research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. OGSv1.1 is an integration of automatic gene predictions from Maker (performed by Dan Hughes at Baylor College of Medicine) with manual annotations by the research community (done via the Apollo manual annotation software). The coordinates of OGSv1.1 were converted to the latest genome assembly, <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000500325.1">GCF_000500325.1</a>, using <a href="https://github.com/NAL-i5K/coordinates_conversion">coordinates_conversion</a> and <a href="https://github.com/NAL-i5K/remap-gff3">remap-gff3</a>, to generate OGSv1.2.</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: Leptinotarsa decemlineata Official Gene Set OGSv1.2.</p> <p>File Name: lepdec_OGSv1-2.tar.gz</p><p>Resource Description: The attached tar.gz archive (lepdec_OGSv1-2.tar.gz) contains the following files: * lepdec_OGSv1.2_GCF_000500325.1_cds.fa - CDS sequences for OGSv1.2 * lepdec_OGSv1.2_GCF_000500325.1_pep.fa - protein sequences for OGSv1.2 * lepdec_OGSv1.2_GCF_000500325.1_trans.fa - transcript sequences for OGSv1.2 * lepdec_OGSv1.2_GCF_000500325.1.gff3 - GFF3 file for OGSv1.2 * lepdec_OGSv1.2_GCF_000500325.1_removed-features.tsv - a list of features removed between OGSv1.1 and OGSv1.2. The list includes feature type, ID, Name, and owner. * lepdec_OGSv1.2_GCF_000500325.1_update-summary.tsv - summary statistics of the features removed between OGSv1.1 and OGSv1.2 </p></li></ul> |
| distribution |
[
{
"@type": "dcat:Distribution",
"title": "lepdec_OGSv1-2.tar.gz",
"format": "gz",
"mediaType": "application/x-gzip",
"downloadURL": "https://ndownloader.figshare.com/files/44572081"
}
]
|
| identifier | 10.15482/USDA.ADC/1457533 |
| keyword |
[
"Colorado Potato Beetle",
"Insects",
"Leptinotarsa decemlineata",
"Organism project",
"i5k"
]
|
| license | https://creativecommons.org/licenses/by-sa/4.0/ |
| modified | 2025-11-21 |
| programCode |
[
"005:040"
]
|
| publisher |
{
"name": "Agricultural Research Service",
"@type": "org:Organization"
}
|
| spatial |
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|
| temporal | 2018-01-01/2018-01-01 |
| title | Leptinotarsa decemlineata Official Gene set v1.2 |
