replying to: E. Leushkin & H. Kaessmann Nature Ecology & Evolution https://doi.org/10.1038/s41559-024-02513-6 (2024)

We acknowledge the commentary by Leushkin and Kaessmann¹ on our work². While we are in agreement on the evolving nature of defining de novo genes with ribosome profiles, we respectfully disagree with their assertions regarding the definition of ages, de novo status, translation and functions of these genes. Notably, the common definition of de novo genes in the field is based on the age of the open reading frames (ORFs), rather than that of the loci^3,4,5,6. Moreover, although ribosome profiles are indicative of translation, the profiles derived from a limited range of temporospatial conditions do not necessarily establish a ground truth for the robust translation and functions of de novo genes. Here we present additional data and analyses to counter their assertions, particularly verifying the status of these new genes and providing compelling evidence for in vivo translation of the case gene. The data presented here, together with those from our initial report, clearly verify our original conclusions.

replying to: E. Leushkin & H. Kaessmann Nature Ecology & Evolution https://doi.org/10.1038/s41559-024-02513-6 (2024)

我们感谢 Leushkin 和 Kaessmann¹ 对我们的工作² 的评论。虽然我们同意定义具有核糖体谱的从头基因的进化性质，但我们尊重地不同意他们关于年龄定义、从头状态、翻译和这些基因功能的断言。值得注意的是，该领域中从头基因的常见定义是基于开放阅读框 （ORF） 的年龄，而不是基因座^3,4,5,6 的年龄。此外，尽管核糖体谱表示翻译，但从有限范围的时间空间条件得出的谱不一定为从头基因的稳健翻译和功能建立基本事实。在这里，我们提供了额外的数据和分析来反驳他们的断言，特别是验证了这些新基因的状态，并为 case 基因的体内翻译提供了令人信服的证据。这里提供的数据以及我们初步报告中的数据清楚地验证了我们最初的结论。