iBeetle
The source of the iBeetle-Base project was the large scale RNAi screen in Tribolium castaneum. Each single gene has been knock down by RNA interference (RNAi) and the phenotype has been annotated following a screening protocol. The results are published in iBeetle-Base. Since than, the database developed to the central information resource for the Tribolium community and beyond.
The biological background
The red flour beetle Tribolium castaneum is a new model organism to study insect development and development in general. Most of what is known about insect gene function is based on Drosophila melanogaster work. Tribolium is a representative of the most species rich animal taxon on earth, the coleopterans, and in many respects the biology of Tribolium is more representative for insects than Drosophila. The segmentation proceeds from a posterior growth zone, the larval head is not involuted and some organs of interst are not present in Drosophila (e.g. defensive stink gland).
The toolbox of Tribolium offers the powerful options of RNAi.
The beetle shows a particulary strong systemic RNAi response. Knockdown phenotypes can be induced in all life stages and spreads througout the animal and is transferred to the offspring.
The iBeetle screen
In two DFG funded screening periods around 8,000 genes have been targeted, reaching a genome coverage of around 50% [1]. The cuticle phenotypes of the remaining genes are subject of a third, industry funded, screening project.
Two screens were performed by injection of dsRNAs into pupal and larval stage, which allowed efficient screening of several biological processes (e.g. metamorphosis, oogenesis, cuticle phenotypes, muscle and stink gland development).The screen allowed to overcome the restrictions by the candidate gene approach and enables the identification of novel players required for long studied processes.
More information about the screening project can also be found on the project web site.
The iBeetle-Base
The annotated phenotypes of the screen has been recorded and published in iBeetle-Base to publish them for the community [2]. The phenotypic data are modeled and stored as triplets of "entity", "qualifier" and "modifier" (EQM) to save which anatomical entity (e.g. coxa) is affected, what is changed (e.g. size) and how (e.g. reduced). The entity is also linked to the Tribiolium Ontology (TrOn) to facilitate a semantic search of specific annotations using an abstract search term [3].
In addition to the phenotypic data of the screeing projects, iBeetle-Base soon started to collected more data, like basic genomic data for all genes, genome browsers or ortholog genes. Lately, we also started to build up a query pipeline to flexible handle sets of data like a list of different expressed genes or GO terms [4].
The future of iBeetle-Base
Currently, we are developing iBeetle-Base from project-specific database to a information resource for the community of developmental biology. The monolithic web application is split up in a set of microservices, each providing its data through an application neutral API. This will free the data and make it available to any application and workflow. The web interface will be re-implemented as single page application serving as first client of the new data-API.
To get new insights of the data and start with some cross-species analysis we will initiate several research projects.
The project is a cooperation between:
- The Dept. of Evolutionary Developmental Genetics
- The Department of Medical Bioinformatics
- The State and University library (SUB)
- The computing center GWDG
Involved people and job offers
Currently are working on the project:
- Jürgen Dönitz
- Karly Conrads
- Malte Vosskamp
To complete the team we are searching for:
- A PhD student for the backend project and the cross-species research
- A student assistant who helps us to implement the new webinterface in JavaScript
If you are interested or have questions, please don't hesitate to contact Jürgen Dönitz!
Publications
[1] Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, et al.
The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.
Nat Commun. 2015;6:7822. doi: doi: 10.1038/ncomms8822.
[2] Dönitz J, Schmitt-Engel C, Grossmann D, Gerischer L, Tech M, Schoppmeier M, et al.
iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum.
Nucleic Acids Res. 2015;43:D720–5. doi: doi: 10.1093/nar/gku1054
[3] Dönitz J, Grossmann D, Schild I, Schmitt-Engel C, Bradler S, Prpic N-M, et al.
TrOn: an anatomical ontology for the beetle Tribolium castaneum.
PloS One. 2013;8:e70695. doi: 10.1371/journal.pone.0070695.
[4] Dönitz J, Gerischer L, Hahnke S, Pfeiffer S, Bucher G.
Expanded and updated data and a query pipeline for iBeetle-Base.
Nucleic Acids Res. 2018;46:D831–5. doi:10.1093/nar/gkx984