Agrilus planipennis community manual annotations

Manual annotation at the i5k Workspace@NAL (https://i5k.nal.usda.gov) is the review and improvement of gene models derived from computational gene prediction. Community curators compare an existing gene model to evidence such as RNA-Seq or protein alignments from the same or closely related species and modify the structure or function of the gene accordingly, typically following the i5k Workspace@NAL manual annotation guidelines (https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project). If a gene model is missing, the annotator can also use this evidence to create a new gene model. Because manual annotation, by definition, improves or creates gene models where computational methods have failed, it can be a powerful tool to improve computational gene sets, which often serve as foundational datasets to facilitate research on a species.Here, community curators used manual annotation at the i5k Workspace@NAL to improve computational gene predictions from the dataset Agrilus planipennis genome annotations v0.5.3. The i5k Workspace@NAL set up the Apollo v1 manual annotation software and multiple evidence tracks to facilitate manual annotation. From 2014-10-20 to 2018-07-12, five community curators updated 263 genes, including developmental genes; cytochrome P450s; cathepsin peptidases; cuticle proteins; glycoside hydrolases; and polysaccharide lyases. For this dataset, we used the program LiftOff v1.6.3 to map the manual annotations to the genome assembly GCF_000699045.2. We computed overlaps with annotations from the RefSeq database using gff3_merge from the GFF3toolkit software v2.1.0. FASTA sequences were generated using gff3_to_fasta from the same toolkit. These improvements should facilitate continued research on Agrilus planipennis, or emerald ash borer (EAB), which is an invasive insect pest.While these manual annotations will not be integrated with other computational gene sets, they are available to view at the i5k Workspace@NAL (https://i5k.nal.usda.gov) to enhance future research on Agrilus planipennis.

Data and Resources

Field Value
accessLevel public
bureauCode {005:18}
catalog_@context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
catalog_conformsTo https://project-open-data.cio.gov/v1.1/schema
catalog_describedBy https://project-open-data.cio.gov/v1.1/schema/catalog.json
identifier 10.15482/USDA.ADC/25076114.v1
license https://creativecommons.org/licenses/by/4.0/
modified 2024-11-19
programCode {005:040}
publisher Agricultural Research Service
resource-type Dataset
source_datajson_identifier true
source_hash a1ab4ff726c483f21b0bcd5660ec991e17cf9056f6f4e5de57bb8f884ee701b4
source_schema_version 1.1
temporal 2014-10-20/2024-01-26
Groups
  • AmeriGEOSS
  • National Provider
  • North America
Tags
  • AmeriGEO
  • AmeriGEOSS
  • CKAN
  • GEO
  • GEOSS
  • National
  • North America
  • United States
  • agrilus-planipennis
  • coleoptera
  • emerald-ash-borer
  • genome-annotation
  • manual-annotation
isopen True
license_id cc-by
license_title Creative Commons Attribution
license_url http://www.opendefinition.org/licenses/cc-by
maintainer Poelchau, Monica, F.
maintainer_email Monica.poelchau@usda.gov
metadata_created 2025-09-29T14:50:46.644392
metadata_modified 2025-09-29T14:50:46.644399
notes <p dir="ltr">Manual annotation at the i5k Workspace@NAL (<a href="https://i5k.nal.usda.gov/" target="_blank">https://i5k.nal.usda.gov</a>) is the review and improvement of gene models derived from computational gene prediction. Community curators compare an existing gene model to evidence such as RNA-Seq or protein alignments from the same or closely related species and modify the structure or function of the gene accordingly, typically following the i5k Workspace@NAL manual annotation guidelines (<a href="https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project" target="_blank">https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project</a>). If a gene model is missing, the annotator can also use this evidence to create a new gene model. Because manual annotation, by definition, improves or creates gene models where computational methods have failed, it can be a powerful tool to improve computational gene sets, which often serve as foundational datasets to facilitate research on a species.</p><p dir="ltr">Here, community curators used manual annotation at the i5k Workspace@NAL to improve computational gene predictions from the dataset <i>Agrilus planipennis</i> genome annotations v0.5.3. The i5k Workspace@NAL set up the Apollo v1 manual annotation software and multiple evidence tracks to facilitate manual annotation. From 2014-10-20 to 2018-07-12, five community curators updated 263 genes, including developmental genes; cytochrome P450s; cathepsin peptidases; cuticle proteins; glycoside hydrolases; and polysaccharide lyases. For this dataset, we used the program LiftOff v1.6.3 to map the manual annotations to the genome assembly GCF_000699045.2. We computed overlaps with annotations from the RefSeq database using gff3_merge from the GFF3toolkit software v2.1.0. FASTA sequences were generated using gff3_to_fasta from the same toolkit. These improvements should facilitate continued research on <i>Agrilus planipennis</i>, or emerald ash borer (EAB), which is an invasive insect pest.</p><p dir="ltr">While these manual annotations will not be integrated with other computational gene sets, they are available to view at the i5k Workspace@NAL (https://i5k.nal.usda.gov) to enhance future research on <i>Agrilus planipennis.</i></p>
num_resources 1
num_tags 13
title Agrilus planipennis community manual annotations