U.S. flag

An official website of the United States government

Ag Data Commons Maintenance - Friday 03/31/23

The Ag Data Commons website and application may experience brief, intermittent outages due to network issues. Avoid adding or editing datasets during this period to prevent losing information.. We apologize for the inconvenience. This notice will be removed once the issue is resolved.

i5k Workspace

About the i5k Workspace@NAL

The i5k Workspace (https://i5k.nal.usda.gov) is an inclusive genome portal for any arthropod genome project that would like to make use of our resources. We provide download services, BLAST, the JBrowse genome browser, and the Apollo manual curation service. Over 50 arthropod genomes are now part of the i5k Workspace, and users are encouraged to browse the genomes that we host, and contribute to the curation of each genome. For more information about the i5k Workspace, you can read our paper on the i5k Workspace, view our posters and talks, and find our software projects on github. The Ag Data Commons is now hosting a growing number of i5k Workspace datasets.

About the i5k initiative

The i5k initiative is a transformative project that aims to sequence and analyze the genomes of 5,000 arthropod species. The National Agricultural Library has partnered with the i5k initiative to create the i5k Workspace@NAL, which serves any ‘orphaned’ arthropod genome project's hosting needs. For more information about the i5k initiative, read the paper and visit the website.

Filter by Author

Filter by Funding Source

Filter by User-supplied tags

i5k Datasets

93 datasets

Genes of viral origin in the Fopius arisanus genome

    *Fopius arisanus* (Sonan) is a braconid wasp (subfamily Opiinae) and biological control agent of a broad range of tephritid fruit fly species, including the global pests Mediterranean fruit fly *Ceratitis capitata* and the Oriental fruit fly *Bactrocera dorsalis*. In an effort to create foundational genomic resources for this species, the complete genome and transcriptomes for several wasp life stages have been recently generated. Manual annotation of 55 viral genes and phylogenetic analysis revealed that *F. arisanus* has independently acquired a symbiotic virus related to alpha-nudiviruses.

    Genes of viral origin in the Microplitis demolitor genome

      *Microplitis demolitor* (Hymenoptera: Braconidae) is a parasitoid used as a biological control agent to control larval-stage Lepidoptera and serves as a model for studying the function and evolution of symbiotic viruses in the genus Bracovirus. Using RNA-Seq data for this species and manual annotation of genes of viral origin, we annotated a high-quality gene set including 171 virus-derived protein-coding genes.

      Microplitis demolitor Official Gene Set micdem_OGSv1.0

        This dataset presents the *Microplitis demolitor* Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from *Microplitis demolitor* genome annotations NCBI-RefSeq's gene set NCBI Microplitis demolitor Annotation Release 101, with manual annotations by the research community, performed via the Apollo manual curation software. Manual annotations were QC'd via the GFF3toolkit and NCBI's table2asn_GFF software, and merged with NCBI Microplitis demolitor Annotation Release 101 via the GFF3toolkit.

        Ephemera danica manual annotations on genome assembly Edan_1.0

          This dataset presents manual annotations of Ephemera danica genome annotations v0.5.3 and genome assembly v1.0. Manual annotations were performed by individual annotators in the Apollo software at the i5k Workspace@NAL, and QC'd via the GFF3toolkit software and manual inspection. Manual annotations are presented here on the original coordinate system of genome assembly v1.0.

          Ephemera danica Official Gene Set ephdan_OGSv1.0

            This dataset presents the *Ephemera danica* Official Gene Set (OGS) v1.0. The OGS is an integration of automatic gene predictions from *Ephemera danica* genome annotations v0.5.3, with manual annotations by the research community. Manual and automated annotations were lifted over from genome assembly *Ephemera danica* genome assembly v1.0 to genome assembly Edan_2.0 using the coordinates_conversion and remap-gff3 programs.

            Leptinotarsa decemlineata genome annotations v0.5.3

              This dataset presents the Leptinotarsa decemlineata gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Leptinotarsa decemlineata genome assembly 1.0.

              Leptinotarsa decemlineata genome assembly 1.0

                This dataset presents the Leptinotarsa decemlineata genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the [National Center for Biotechnology Information's GenBank resource](http://www.ncbi.nlm.nih.gov/assembly/GCA_000696205.1)