Gene Data Tables from: <i>Pangenomics Links Boll Weevil Divergence with Ancient Mesoamerican Cotton Cultivation</i>
These supplementary data tables represent gene annotations, gene ontology terms (GO), and gene coordinates from the boll weevil (Anthonomus grandis grandis, Agg) reference genome that appear in selectively swept regions and structural variations between the subspecies Agg and Agt (Anthonomus grandis thurberia). These genes were determined from two computer programs for selective analysis: RAiSD and PCAdapt. The gene tables are organized by shared/unique genes per sub-species and shared/unique genes residing on SVs, structural variations, per sub-species, which is based on >80% sequence identity. These data provide supplementary details for the enrichment tests that were carried out to associate gene function with subspecies biology, described in more detail in the manuscript: Pangenomics Links Boll Weevil Divergence with Ancient Mesoamerican Cotton Cultivation. This work is relevant to cotton managers throughout United States cotton growing regions, our international collaborators, as well as genome biologists investigating structural changes in genome architecture and their association with adaptation and trait plasticity.
Resources
6 resources available
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Shared_genes_AGGAGT_svs.csv
CSV -
Unique_genes_AGG_svs.csv
CSV -
Unique_genes_AGT_svs.csv
CSV -
Shared_Outlier_AggAgt_PCAdapt_RAiSD.csv
CSV -
Outlier_Agt_PCAdapt_RAiSD.csv
CSV -
Outlier_Agg_PCAdapt_RAisD.csv
CSV
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "005:18" ] |
| contactPoint |
{ "fn": "Perkin, Lindsey", "hasEmail": "mailto:lindsey.perkin@usda.gov" } |
| description | <p dir="ltr">These supplementary data tables represent gene annotations, gene ontology terms (GO), and gene coordinates from the boll weevil (Anthonomus grandis grandis, Agg) reference genome that appear in selectively swept regions and structural variations between the subspecies Agg and Agt (Anthonomus grandis thurberia). These genes were determined from two computer programs for selective analysis: RAiSD and PCAdapt. The gene tables are organized by shared/unique genes per sub-species and shared/unique genes residing on SVs, structural variations, per sub-species, which is based on >80% sequence identity. These data provide supplementary details for the enrichment tests that were carried out to associate gene function with subspecies biology, described in more detail in the manuscript: Pangenomics Links Boll Weevil Divergence with Ancient Mesoamerican Cotton Cultivation. This work is relevant to cotton managers throughout United States cotton growing regions, our international collaborators, as well as genome biologists investigating structural changes in genome architecture and their association with adaptation and trait plasticity. </p> |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Shared_genes_AGGAGT_svs.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/49594398" }, { "@type": "dcat:Distribution", "title": "Unique_genes_AGG_svs.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/49594401" }, { "@type": "dcat:Distribution", "title": "Unique_genes_AGT_svs.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/49594404" }, { "@type": "dcat:Distribution", "title": "Shared_Outlier_AggAgt_PCAdapt_RAiSD.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/49594416" }, { "@type": "dcat:Distribution", "title": "Outlier_Agt_PCAdapt_RAiSD.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/49594419" }, { "@type": "dcat:Distribution", "title": "Outlier_Agg_PCAdapt_RAisD.csv", "format": "csv", "mediaType": "text/csv", "downloadURL": "https://ndownloader.figshare.com/files/49594425" } ] |
| identifier | 10.15482/USDA.ADC/27158388.v1 |
| keyword |
[ "boll weevil management", "gene list selection" ] |
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2026-02-12 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2024-10-02/2024-10-02 |
| title | Gene Data Tables from: <i>Pangenomics Links Boll Weevil Divergence with Ancient Mesoamerican Cotton Cultivation</i> |
