Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster

Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in de novo gene emergence. However, little is known about the rates at which de novo transcripts are gained and lost in individuals of the same species. Here, we address this gap and estimate for the first time the de novo transcript turnover rate. We use DNA long reads and RNA short reads from seven samples of inbred individuals of Drosophila melanogaster to detect de novo transcripts that are (transiently) gained on a short evolutionary time scale. Overall, each sampled individual contains between 2,320 and 2,809 unspliced de novo transcripts with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5×10−5 per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rates provide first empirical estimates to better predict and comprehend the process of de novo gene birth.