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Abstract

Background: Genes can arise not only through the modification of existing genes but also entirely from scratch. For this to occur, these de novo genes need to gain the necessary mutations to be transcribed, as well as acquire an open reading frame (ORF) that enables translation into a protein. The exact mechanisms that allow de novo genes to emerge from noncoding regions of the genome are not fully understood. This is also true for the frequency at which they emerge, spread within a population, and eventually achieve functionality. Furthermore, studying de novo genes can be challenging due to inconsistencies between detection pipelines or quality differences between ingroup and outgroup genomes. These problems can lead to inaccurate estimates regarding the age or quantity of de novo genes. Methods: Here, we aim to explore the dynamics of de novo gene emergence by sequencing the genomes and transcriptomes of multiple populations across six Drosophila species with divergence times of up to 40 million years. To overcome previous challenges, we employ a consistent assembly and annotation strategy. Our focus lies especially on studying the early stages of de novo gene emergence. To do this, we made use of DESwoMAN, a recently developed pipeline designed to identify newly-evolved expressed ORFs (neORFs) from transcriptomes. Results: We show that neORFs are predominantly specific to a single species, though a subset is shared across several of them. Moreover, we find that neORFs differ from protein-coding genes in several features such as length, GC content, and expression level. Finally, we identified their noncoding homologs in outgroup genomes which enabled us to examine the mutations allowing these neORFs to emerge. Conclusion: In conclusion, neORFs exhibit distinct features compared to protein-coding genes. Additionally, the frequency of mutations in their noncoding homologs increases with phylogenetic distance, though not all of them are equally common. Taken together our results provide new insights into the early stages of de novo gene emergence.