Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster

Abstract

Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines ofDrosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.

DE Novo emerged gene SEarch in Eukaryotes with DENSE

“…Yet, the fractions of de novo emerged genes conserved beyond the focal species remain very low (23%, 13%, and 13% for O. sativa, M. musculus, and H. sapiens, respectively). We can hypothesize that these genes emerged earlier and were subsequently lost in the sister lineages, recalling the high turnover of novel ORFs reported by Grandchamp et al (Grandchamp et al, 2023); alternatively, they may reflect very young genes that have emerged recently in the lineage of the focal species, or they may simply result from annotation bias. Model organisms may have been over-annotated with respect to their neighbors as it is the case for example with the manual annotation of yeast available in the Saccharomyces Genome Database (Cherry et al, 2012).…”

De novoORFs are more likely to shrink than to elongate during neutral evolution

“…We discarded orthogroups that contained more than one ORF per line. Next, we analysed the genes flanking the ORF of an orthogroup (synteny), using genome annotations for the seven lines (Grandchamp et al, 2023a). If the neighboring genes were identical for all ORFs, we kept them in the same orthogroup, and split them into multiple orthogroups, otherwise.…”

“…Because our study focuses primarily on ORF length extension but not gain and loss of transcription, we included non-transcribed ORFs in our orthogroups, that were homologous and syntenic to the transcribed ORFs the same orthogroup. To this end we adapted the analytical pipeline from Grandchamp et al (2023a). Specifically, we first identified the flanking genes of an orthogroup.…”

DNA Transposons favour denovotranscript emergence through enrichment of transcription factor binding motifs

“…While the gain of ORFs in the emergence of de novo genes has been well studied (Zhuang and Cheng, 2021;Delihas, 2022;Rödelsperger et al, 2019;Wang et al, 2020b;Carvunis et al, 2012;Grandchamp et al, 2023b), how transcription is acquired remains poorly understood.…”

“…For a de novo gene to arise, it requires both the gain of an open reading frame (ORF) and the acquisition of transcription (Durand et al, 2019; Schlötterer, 2015). While the gain of ORFs in the emergence of de novo genes has been well studied (Zhuang and Cheng, 2021; Delihas, 2022; Rödelsperger et al, 2019; Wang et al, 2020b; Carvunis et al, 2012; Grandchamp et al, 2023b), how transcription is acquired remains poorly understood.…”