FOR 1234: iBeetle: Functional Genomics of Insect Embryogenesis and Metamorphosis
Final Report Abstract
Insect gene function has been studied predominantly in the fly Drosophila melanogaster, not least due to the possibility to perform genome wide unbiased genetic screens, which identify genes required for a given biological process. Reverse genetics using RNAi has allowed studying gene function in additional species, where in most cases candidate genes known from Drosophila have been studied. The use of one main model organism complemented with the candidate gene approach in other species has been very successful but has restrictions: (1) Certain biological questions cannot be studied in Drosophila, for instance because the respective process is absent. (2) The candidate gene approach is exhausted for a given process but important components are still missing. (3) Relevant genes may have been missed in Drosophila screens for technical reasons. The aim of the iBeetle project was to overcome these restrictions by establishing the red flour beetle Tribolium castaneum as a second insect model allowing unbiased genome wide screening. In the core projects we have generated enhanced versions of the genomic sequence and the official gene set. We have expanded the iBeetle-Base into a comprehensive database on Tribolium gene information including the iBeetle phenotypes and mutually linked with FlyBase. Further, RNAi resources were produced for at least half of the predicted gene set, a large scale RNAi screen was performed and phenotypes for several processes were annotated for more than 8,500 genes. Based on industrial funding we are currently continuing the screen to cover the remaining 8,000 genes. These resources allow for future mid-scale or genome-wide screens at reasonable effort and cost. In the particular projects, we indeed found gene functions that were missed by the previous candidate gene approach. For example, Tc-germ cell-less was required for anterior patterning, and its knockdown revealed the first genetically induced double abdomen phenotype in short germ insects. In DV patterning, two novel serine proteases were identified for which an involvement in development had not been known. Their analysis indicated that DV patterning is very different from the fly. For head development, we estimate that about 20-25% of the involved genes would have been missed by the candidate gene approaches based on Drosophila and vertebrate data. Importantly, we found novel genes relevant for Drosophila cell biology, for instance genes required for epithelial adhesion and genes required for muscle identity specification and myoblast fusion, which in the fly were overlooked due to genetic redundancies. Novel target genes for RNAi based pest control were identified and inspired industrial funding for the project. In summary, the possibility to study gene function in insect biology has been significantly expanded, which will impact research beyond the iBeetle project with its specific findings. Indeed, researchers of the wider community are starting to use the iBeetle resources for their specific purposes.
Publications
- 2013. RNAi phenotypes are influenced by the genetic background of the injected strain. BMC Genomics 14, 5
Kitzmann, P., Schwirz, J., Schmitt-Engel, C., Bucher, G.
(See online at https://doi.org/10.1186/1471-2164-14-5) - 2013. TrOn: an anatomical ontology for the beetle Tribolium castaneum. PloS One 8, e70695
Dönitz, J., Grossmann, D., Schild, I., Schmitt-Engel, C., Bradler, S., Prpic, N.-M., Bucher, G.
(See online at https://doi.org/10.1371/journal.pone.0070695) - 2015. iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. Nucleic Acids Res. 43, D720–D725
Dönitz, J., Schmitt-Engel, C., Grossmann, D., Gerischer, L., Tech, M., Schoppmeier, M., Klingler, M., Bucher, G.
(See online at https://doi.org/10.1093/nar/gku1054) - 2015. Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target. BMC Genomics 16
Ulrich, J., Dao, V.A., Majumdar, U., Schmitt-Engel, C., Schwirz, J., Schultheis, D., Ströhlein, N., Troelenberg, N., Grossmann, D., Richter, T., Dönitz, J., Gerischer, L., Leboulle, G., Vilcinskas, A., Stanke, M., Bucher, G.
(See online at https://doi.org/10.1186/s12864-015-1880-y) - 2015. The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. Nat. Commun. 6, 7822
Schmitt-Engel, C., Schultheis, D., Schwirz, J., Ströhlein, N., Troelenberg, N., Majumdar, U., Dao, V.A., Grossmann, D., Richter, T., Tech, M., Dönitz, J., Gerischer, L., Theis, M., Schild, I., Trauner, J., Koniszewski, N.D.B., Küster, E., Kittelmann, S., Hu, Y., Lehmann, S., Siemanowski, J., Ulrich, J., Panfilio, K.A., Schröder, R., Morgenstern, B., Stanke, M., Buchhholz, F., Frasch, M., Roth, S., Wimmer, E.A., Schoppmeier, M., Klingler, M., Bucher, G.
(See online at https://doi.org/10.1038/ncomms8822) - 2016. Simultaneous gene finding in multiple genomes. Bioinforma. Oxf. Engl. 32, 3388–3395
König, S., Romoth, L.W., Gerischer, L., Stanke, M.
(See online at https://doi.org/10.1093/bioinformatics/btw494)
