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.
", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/44244485", "format": "gz", "mediaType": "application/x-gzip", "title": "Apla_2.0-manual-annotations-v2024.tar.gz"}], "identifier": "10.15482/USDA.ADC/25076114.v1", "keyword": ["Agrilus planipennis", "Coleoptera", "Emerald ash borer", "Genome annotation", "Manual annotation"], "license": "https://creativecommons.org/licenses/by/4.0/", "modified": "2024-11-19", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "temporal": "2014-10-20/2024-01-26", "title": "Agrilus planipennis community manual annotations"}