Project Details
Projekt
Alternative Splicing and the Evolution of Holometaboly
Subject Area
Evolutionary Cell and Developmental Biology (Zoology)
Bioinformatics and Theoretical Biology
Bioinformatics and Theoretical Biology
Term
since 2025
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 570450683
Holometabolous insects, such as beetles, flies, and butterflies, undergo complete metamorphosis, developing larval forms that are markedly different from their adult counterparts. A key feature of this innovation is the existence of two distinct functional brains encoded by the same genome. This project explores the general evolutionary trends of alternative splicing (i.e. the production of multiple mRNA isoforms from a single gene) in the insect clade and specifically tests the hypothesis that alternative splicing was a crucial mechanism enabling the emergence of stage-specific brain structures in the holometabola. To address this, we will generate long-read brain transcriptomes from both larval/nymph and adult stages across a broad range of insect species. This comparative approach will reveal patterns of alternative splicing and assess whether holometabolous insects exhibit a greater degree of stage-specific isoform diversity compared to hemimetabolous species. In-depth developmental transcriptome profiling of the beetle Tribolium castaneum will allow us to identify candidate isoforms that differ between life stages and may have contributed to the divergence of larval and adult brains. Functional experiments will target selected isoforms using isoform-specific RNA interference in Tribolium, testing their role in regulating the formation of two brains from one genome. On the computational side, we will refine and apply genome annotation pipelines to detect stage-specific isoforms across 26 insect genomes. Furthermore, we aim to extend the deep-learning-based gene predictor Tiberius. The extended version shall be able to integrate RNA-Seq from long and short-read technology and jointly model multiple isoforms in a locus. The development of this new method shall improve both the annotation of newly sequenced genomes and our understanding of how novel isoforms arise. By integrating evolutionary genomics, developmental biology, and deep learning, this project will provide a comprehensive view of the role of alternative splicing in the origin of insect metamorphosis. The results will not only clarify the molecular mechanisms behind a major evolutionary innovation but also deliver valuable resources and methods for the broader genomics community.
DFG Programme
Priority Programmes
