Extent, speed, and causes of changes in the protein-coding gene repertoire of holometabolous insects (Insecta: Endopterygota)

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Most phenotypic differences between species are the manifestation of differences between genomes. While the evolution of organismic diversity is often interpreted as evolution of regulatory networks, changes in the species' gene repertoire could also have significantly contributed to the evolution of this diversity. In fact, genome sequencing projects have led to the unexpected insight that, in eukaryotes, virtually every species harbors a rich set of seemingly species-specific protein-coding genes. This result implies that gene turnover (GT) could be an underrated factor in the evolution of organismic diversity. However, robust inference of GT rates and identification of genomic factors and mechanisms that cause GT rate changes require a dense and representative sampling of sequenced genomes as well as knowledge of the phylogenetic relationships and divergence times of the respective species. Such data sets have been sparse, which hampered examining the role of GT in the genomes of insects, arguably the most diverse lineage of animals (given their phylogenetic age). To obtain a better understanding of GT as an important and general aspect of genome dynamics, we invested into compiling comprehensive genomic and phylogenetic data, which form the basis for the research project outlined here. Specifically, we de novo sequenced the genomes of 33 insect species, representing almost all major lineages of holometabolous insects, and inferred a robust insect backbone tree of life including reliable divergence time estimates. Exploiting this unique set of data, we will estimate GT rates in insect genomes and assess the most promising genomic factors that could cause GT rate changes: non-homologous (ectopic) recombination mediated by the presence and propagation of transposable elements (TEs) and whole genome duplication (WGD). To infer the historic occurrence of these events, we will determine the repertoires and diversification histories of protein-coding genes and TEs and search for genome-wide simultaneous expansions of gene families. Finally, we will assess whether changes in TE abundance and/or WGD correlate with GT rate changes. The outcome of our proposed study will shed new light on the dynamics of GT rates in insect genomes and on mechanisms and factors that likely cause them. Since the gene repertoire is a fundamental property of an organism's genome, our results will be of major interest for researchers in various research fields, ranging from evolutionary biology and comparative genomics to developmental biology and biodiversity research.