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Abstract

Our understanding of development is largely derived from morphological insights with data collections reaching back to the time of Aristotle. Sequencing the (epi-)genomes and annotating the protein sequences across the tree of life is currently transforming our access to the molecular principles of development and biodiversification. The key to accessing this reservoir of genomic information for molecular exploration and functional annotation is the comparative method, now enabled by sequence similarity assessments at tree-of-life scale in combination with developmental transcriptomics. An emerging question of the past decades enabled by these molecular quantification techniques is: how do gene regulatory programs control the formation of multicellular body structures across all kingdoms of life? In particular, there is initial evidence that ancient genes, that is genes with possible evolutionary origin in the last common ancestors of eukaryotes, bacteria, and archaea are dominating the mRNA pool (transcriptome) and epigenetic landscape at crucial developmental transitions during multicellularity formation. We introduce the scientific software DIAMOND2, DIAMOND2 DeepClust, GenEra, and myTAI and explore how they can be employed to unveil such evolutionary transcriptomics patterns for further experimental investigation. Finally, we discuss whether these convergent evolutionary transcriptomics patters share some universal principles of developmental organisation.