Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster 48149, Germany.
Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen 72076, Germany.
Genome Biol Evol. 2024 Jul 3;16(7). doi: 10.1093/gbe/evae129.
For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed a mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations are also in agreement with the model's prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. Alternatively, shorter ORFs may be purged because they may be less likely to yield functional proteins.
为了使蛋白质编码基因从非基因 DNA 中全新出现，该 DNA 序列必须获得开放阅读框 (ORF) 和转录能力。新出现的全新基因可以进一步进化，从而在其序列中积累变化。因此，它也会随着时间的推移而延长或缩短。现有文献表明，较老的全新基因具有更长的 ORF，但尚不清楚它们是随着时间的推移而延长，还是从出现以来一直保持相同的长度。为了解决这个问题，我们开发了一个 ORF 延长的马尔可夫跳跃过程的数学模型，并表明 ORF 在短的进化时间尺度上倾向于保持其长度。我们还表明，如果发生变化，很可能是截短。我们对 7 个黑腹果蝇种群的基因组学和转录组学数据分析也与模型的预测一致。我们的结论是，选择可能促进 ORF 长度的延伸，这可以解释为什么在分析更长进化时间尺度的研究中观察到较长的 ORF 出现在较老的全新基因中。或者，较短的 ORF 可能被清除，因为它们不太可能产生功能蛋白。
