Ladona fulva Official Gene Set ladful_OGSv1.0

This dataset presents the Ladona fulva Official Gene Set (OGS) v1.0. The OGS v1.0 is an integration of automatic gene predictions from Ladona fulva genome annotations v0.5.3 (https://10.15482/USDA.ADC/1503790), with manual annotations by the research community (https://data.nal.usda.gov/dataset/ladona-fulva-manual-annotations-genome..., performed via the Apollo manual curation software, http://genomearchitect.org/). Manual and automated annotations were lifted over from genome assembly Ladona fulva genome assembly v1.0 (https://10.15482/USDA.ADC/1503789) to genome assembly Lful_2.0 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000376725.2) using the coordinates_conversion and remap-gff3 programs (https://github.com/NAL-i5K/coordinates_conversion/; https://github.com/NAL-i5K/remap-gff3) and mapping files generated by NCBI's Genome remapping service (https://www.ncbi.nlm.nih.gov/genome/tools/remap). 1,015 annotations were removed from the original datasets during this process, due to changes in the new genome assembly, or due to quality problems with the original gene models. Identifiers and names for these gene models are listed in this file: deleted_models.txt.

The OGS v1.1 differs from OGS v1.0 in that it contains NCBI GenBank protein accession numbers. The GenBank accession GCA_000376725.2 also contains these annotations.

More information about this dataset can be found here:
https://doi.org/10.1186/s13059-019-1925-7

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Ladona fulva Official Gene Set ladful_OGSv1.0Data
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Field	Value
Tags	genome annotation Ladona fulva
Modified	2022-05-25
Release Date	2021-02-18
Identifier	fd70b3a9-f5ca-4b4d-9629-9e50ee0c1477
Spatial / Geographical Coverage Area	POINT (49.66667 7.5)
Publisher	Ag Data Commons
Spatial / Geographical Coverage Location	Rheinland-Pfalz, Germany
Temporal Coverage	May 7, 2011
License	Creative Commons Attribution Share-Alike
Contact Name	Poelchau, Monica
Contact Email	monica.poelchau@usda.gov
Public Access Level	Public

Extended Metadata:

Field	Value
Authors	Provataris, Panagiotis (Scopus Author ID) Ahn, Seung-Joon (ORCID) Futahashi, Ryo (ORCID) Jones, Jeffery (Scopus Author ID) Niehuis, Oliver (ORCID) Robertson, Hugh M. (ORCID) Southgate, Agnes (Scopus Author ID) Poelchau, Monica (ORCID) Hughes, Daniel S.T. (Scopus Author ID) Richards, Stephen (ORCID)
Peer Reviewed	No
Equipment or Software Used	GFF3toolkit software Apollo manual curation software remap-gff3 software coordinates_conversion software
Funding Sources	National Human Genome Research Institute U54 HG003273
Related Articles	Thomas, G. W. C., Dohmen, E., Hughes, D. S. T., Murali, S. C., Poelchau, M., Glastad, K., Anstead, C. A., Ayoub, N. A., Batterham, P., Bellair, M., Binford, G. J., Chao, H., Chen, Y. H., Childers, C., Dinh, H., Doddapaneni, H. V., Duan, J. J., Dugan, S., Esposito, L. A., Friedrich, M., Garb, J., Gasser, R. B., Goodisman, M. A. D., Gundersen-Rindal, D. E., Han, Y., Handler, A. M., Hatakeyama, M., Hering, L., Hunter, W. B., Ioannidis, P., Jayaseelan, J. C., Kalra, D., Khila, A., Korhonen, P. K., Lee, C. E., Lee, S. L., Li, Y., Lindsey, A. R. I., Mayer, G., McGregor, A. P., McKenna, D. D., Misof, B., Munidasa, M., Munoz-Torres, M., Muzny, D. M., Niehuis, O., Osuji-Lacy, N., Palli, S. R., Panfilio, K. A., Pechmann, M., Perry, T., Peters, R. S., Poynton, H. C., Prpic, N.-M., Qu, J., Rotenberg, D., Schal, C., Schoville, S. D., Scully, E. D., Skinner, E., Sloan, D. B., Stouthamer, R., Strand, M. R., Szucsich, N. U., Wijeratne, A., Young, N. D., Zattara, E. E., Benoit, J. B., Zdobnov, E. M., Pfrender, M. E., Hackett, K. J., Werren, J. H., Worley, K. C., Gibbs, R. A., Chipman, A. D., Waterhouse, R. M., Bornberg-Bauer, E., Hahn, M. W., & Richards, S. (2020). Gene content evolution in the arthropods. Genome Biology, 21(1). https://doi.org/10.1186/s13059-019-1925-7
Dataset DOI (digital object identifier)	10.15482/USDA.ADC/1520869
Product Type	Dataset
Related Content	Ladona fulva genome assembly v1.0 Ladona fulva genome annotations v0.5.3 Generic sample from Ladona fulva HasVersion: Ladona fulva Official Gene Set ladful_OGSv1.1

Field	Value
OSTI Identifier
ISO Topic(s)	biota
National Agricultural Library Thesaurus Term	genomics genes prediction genome assembly Biological Sciences Ladona fulva Insects and Entomology
Ag Data Commons Keywords	Genomics & Genetics Genome Genome annotation Genomics & Genetics Genome Genomics & Genetics
Program	Ladona fulva Organism project Insects 5K – i5K

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