New Insect Genome-Hosting Resource

Kim Paczolt, Ph. D., postdoctoral researcher, Department of Biology, University of Maryland College Park.

Kim Paczolt, Ph. D., Postdoctoral Researcher, Department of Biology, University of Maryland College Park.

The 5000 arthropod genomes initiative (i5k) has announced its new online genome repository, the i5k Workspace@NAL, in a paper in Nucleic Acids Research (Poelchau et al 2014).

The Workspace@NAL, hosted at the National Agricultural Library, promises to be a useful resource for a wide variety of researchers.

The aim of the i5k initiative is to sequence 5000 insect and other arthropod genomes over 5 years (Evans et al. 2013).

The Workspace@NAL will provide an online repository for researchers to access these data. The initial roll-out includes 35 existing arthropod genomes, 29 of which were sequenced during the i5k initiative pilot project.

Researchers may make use of the Workspace@NAL in two ways: 1) as a repository to share their own genomic resources or 2) as a resource to access the genomes of a diverse array of arthropods.

5000 Insect Genomes Initiative

i5k participants can submit and share their genomic resources on the Workspace@NAL.  In addition to a genome assembly, participants can submit supplemental data, such as transcriptomes, RNA-Seq mapping (using iPlant), and genome annotation.

Once hosted on the Workspace@NAL, registered members of your research community can collaboratively annotate and edit your posted genome using Web Apollo software.

It is important to note that the Workspace@NAL acts as a repository only. The i5k initiative will provide some advice in tailoring the content to your research community’s needs but will not contribute directly to the annotation of genomes submitted by outside researchers. This marks an important distinction between the Workspace@NAL and other genome portals, such as Ensembl, in which annotation is standardized and completed by the database team rather than the originating researcher.

Apollo On The Web

Web Apollo

Generic Model Organism Database project

J Browse is part of the Generic Model Organism Database project

JBrowse: Super-fast genome annotation viewer

Users interested in accessing the posted data have several user-friendly options.  Researchers who wish to visualize the genomic resources available for one species can do so using JBrowse. Alternatively, the Workspace@NAL makes BLAST+ available for users interested in searching all of the genomes simultaneously. All data hosted on the Workspace@NAL is also available for download through the web browser.

With the rapid accumulation of insect genome data, one can find genome resources for many insect species all over the internet.   Having a central resource in which data can be deposited and collectively annotated could help to allow these valuable data to be more easily found and used.

 

Poelchau, M., Childers, C., Moore, G., Tsavatapalli, V., Evans, J., Lee, C. Y., Lin, H., Lin J.W., & Hackett, K. 2014. The i5k Workspace@ NAL—enabling genomic data access, visualization and curation of arthropod genomes. Nucleic acids research, doi: 10.1093/nar/gku983.

 

Other References Cited.

Evans, J. D., Brown, S. J., Hackett, K. J., Robinson, G., Richards, S., Lawson, D., Elsik, C., Coddington, J., Edwards, O., Emrich, S., Gabaldon, T., Goldsmith, M., Hanes, G., Misof, B., Munoz-Torres, M., Niehuis, O., Papanicolaou, A., Pfrender, M., Poelchau, M., Purcell-Miramontes, M., Robertson, H. M., Ryder, O., Tagu, D., Torres, T., Zdobnov, E., Zhang, G. J., Zhou, X. & Consortium, i. K. 2013. The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health,Agriculture, and the Environment i5K CONSORTIUM. Journal of Heredity 104: 595-600.

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