standard Knocking Down All Beetle Genes – iBeetle

Nathaniel Grubbs, Ph.D.

Nathaniel Grubbs, Ph.D., Department of Entomology, North Carolina State University
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Dönitz, et al. (2015) recently published a paper describing iBeetle-Base, a repository for the results of the iBeetle screen, an effort to target each gene of Tribolium castaneum using RNAi.

Advances in sequencing technology have made more genome data available to the insect community than ever before. But genetic research is hampered by a limited understanding of what many genes do. The best-studied insect, Drosophila melanogaster, has many well-characterized genes, but its developmental is, in many ways, atypical compared to the average insect. The red flour beetle, Tribolium castaneum, has more typical insect development, and has become a useful model for genetic and evolutionary studies. However, more genetic data is needed from this species to provide a broader understanding of gene function and evolution.

The iBeetle screen is an effort to target each gene of Tribolium castaneum using RNAi. So far, the project has knocked down over a third of the beetle’s 16,505 genes, and examined several traits for effects. Because of Tribolium’s robust systemic RNAi response, injections are being done in pupal females to examine both adult and embryonic traits, as well as in larvae, to identify effects in pupae and in adults.

The results of this screen are being compiled in a systematic fashion to enable quick, easy searches for genes or characteristics of interest.

iBeetleBase

iBeetle-Base Start-Page (Screen Shot)

Each gene has its own page, which includes links to RNA and protein sequence, as well as the sequence of the dsRNA(s) used to target it, descriptions and images of phenotypes, and information about known orthologs in Drosophila via links to FlyBase.

Phenotype annotations follow the EQM (entity, quality, modifier) system to establish a consistent way to describe what trait has been effected and how. Consistency is further maintained by the use of the TrOn (Tribolium Ontology) terms for anatomical structures, categorized by both type and life stage. Together, these two systems of annotation are combined to shape the search fields of the iBeetle-Base start page, which allows users to look for RNAi targets that affect morphological traits of interest.

Searches can be broad (ex: appendages), or refined to define a specific alteration of a specific anatomical part for a specific life stage (ex: decreased size of adult prothoracic leg). The site also provides data about penetrance of the RNAi affect, which can serve as a proxy for filtering possible false positives (higher penetrance is less likely to be a false positive).

It is the hope of the iBeetle-Base community to provide a bridge between well-studied Drosophila and other insect species.

iBeetle Record

iBeetle-Base Record. Screen shot of part of a record showing some of the data contained within each record.

Their intentional approach to categorizing phenotypes of every Tribolium gene are only the start. In addition to continuing the iBeetle screen, they also hope to build links from FlyBase to iBeetle-Base, and to start including community-provided information, such as expression data, and previously described and newly discovered phenotypes.

It is their hope that these resources will become useful to insect researchers beyond the Tribolium community.

 

Dönitz, J., Schmitt-Engel, C., Grossmann, D., Gerischer, L., Tech, M. et al., 2015 iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. Nucleic Acids Res 43: D720-D725doi: 10.1093/nar/gku1054.

 

 

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