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The Ag Data Commons is migrating

The Ag Data Commons is migrating to a new institutional portal on Figshare. The current system is available for search and download only. The new platform is open for submission with assistance from Ag Data Commons curators. Please contact NAL-ADC-Curator@usda.gov, if you need to publish or update your datasets.

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.

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i5k Datasets

115 datasets

Diaphorina citri Official Gene Set v1.0

    This gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome.

    Hyalella azteca Genome Annotations v0.5.3

      The Baylor College of Medicine recently sequenced and annotated the Hyalella azteca genome as part of the i5k pilot project. This dataset presents the Hyalella azteca 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 Hyalella azteca genome assembly 1.0. Further annotation method details will be available in a forthcoming publication.

      NOTE: This gene set is an unstable pre-release (v0.5.3), and was provided to facilitate manual curation and analyses before the official gene set is released. Gene identifiers from this gene set will likely not be maintained.

      Blattella germanica Official Gene Set OGSv1.0

        The *Blattella germanica* genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The *Blattella germanica* research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0.

        Agrilus planipennis genome annotations v0.5.3

          This dataset presents the Agrilus planipennis gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Agrilus planipennis genome assembly 1.0. This dataset is free for all use.

          Pachypsylla venusta genome annotations v0.5.3

            This dataset presents the Pachypsylla venusta gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Pachypsylla venusta genome assembly 1.0.

            Pachypsylla venusta genome assembly v1.0

              The Baylor College of Medicine has sequenced and annotated the Pachypsylla venusta genome as part of the i5k pilot project. This dataset presents the Pachypsylla venusta 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.

              Anoplophora glabripennis Official Gene Set OGSv1.2

                The *Anoplophora glabripennis* genome was recently sequenced, assembled and annotated as part of the i5k pilot project by the Baylor College of Medicine, in collaboration with the McKenna Laboratory at the University of Memphis. The *Anoplophora glabripennis* research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.2. OGSv1.2 was generated by merging gene set AGLA-c0.5.3-Models generated by the Baylor College of Medicine, and community-curated models in the Apollo software, after QC of the Apollo output.