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Genomics facilitates a remarkable array of studies of cellular processes at the molecular level. The decreasing costs and growing throughput of sequencing are providing unprecedented opportunities within the reach of many research groups. Beyond whole-genome sequencing of particular organisms, extracting and sequencing DNA directly from environmental samples, termed metagenomics, revolutionized our understanding of the microbial complexity and the role of animal’s microbiota in the biology of their hosts. Yet, the insect genomics revolution is still in its infancy, with fewer than 40 sequenced arthropods and only the very first steps being taken towards initiatives to scale it up to 5’000 (the i5K initiative). Importantly, the technology already allows reading the complete genome of insects together with their microbiomes, from fungi to bacteria to viruses, all in one go. Thus, the discovery snapshot we propose here is denoted as (meta)genomics, although understanding of the microbiome dynamics will require more focused longitudinal studies in the future. It is clear, however, that analysis of such tremendous amounts of data requires further elaboration of computational approaches, and the data analysis costs already outweigh the data generation costs, with the biggest analysis challenge being to link genotype-to-phenotype. This project is focused on the study of insects. Insects are the most diverse and successful terrestrial animals, encompassing by far the largest number of species. Thus, insect genomes provide an exceptional opportunity to explore the evolutionary processes acting on genes and genomes to understand how these processes translate into new functions and phenotypes. The overarching question of genotype-to-phenotype mapping remains complex, yet it is becoming more feasible as both genotype and phenotype resources are expanding and the large-effect phenotypes of the incredible adaptations in insects, such as the emergence of wings or metamorphosis, provide a clear starting point.The objectives of this proposal are to: Aim 1:Sequence (meta)genomes of 20 basal insects representing wingless insects (e.g. springtails, bristletails, and silverfish) and basal winged insects (e.g. mayflies, dragonflies, and damselflies) to dramatically improve the genome sampling from this key phyletic radiation point, and to provide the basis for addressing the genotype-to-phenotype question through large-effect cases such as the evolution of flight and metamorphosis; and toAim 2:Advance the state-of-the-art methods in computational (meta)genomics through further development of our comparative toolbox (for analysis of gene orthology, families, ncRNAs, miRNAs and their targets, CNCs, genomic gene arrangements (microsynteny), high throughput phylogenomics, and microbiomes), and the implementation of these tools into pipelines accessible to the research community.World-leading expertise and a reputation for delivering trustworthy results are key requirements sought after by international consortia. In such consortia, my laboratory led the evolutionary analyses of several recently sequenced animal genomes. This experience and established collaborations with the leading researchers in the field present a unique setting for this project, e.g. the biological material will be provided by our collaborators, the project is endorsed by the i5K consortium, and the Baylor College will advise us on sequencing (see the letters of support provided). Although the aims may appear ambitious, we will prioritise our intermediate targets for the highest potential impact.