新的蛋白质编码基因可以通过称为从头基因出现的过程从先前的非编码基因组区域进化。有证据表明,这个过程很可能在整个进化过程中和整个生命树之间发生。然而,自信地识别从头出现的基因仍然具有挑战性。祖先序列重建(ASR)是推断基因是否从头出现的一种有前途的方法,因为它可以使我们检查给定的基因组基因座是否具有祖先的蛋白质编码能力。然而,在从头出现的背景下使用ASR仍处于起步阶段,局限性,总体潜力在很大程度上是未知的。值得注意的是,很难正式评估祖先序列的蛋白质编码能力,特别是当新的候选基因很短的时候。ASR作为检测和研究从头基因的工具有多合适?在这里,我们通过设计包含不同工具和参数集的ASR工作流程,并通过引入允许估计的正式标准来解决这个问题,在理想的信心水平内,当蛋白质编码能力起源于特定基因座时。将此工作流程应用于2,600短,注释出芽酵母基因(<1,000个核苷酸),我们发现ASR有力地预测了最广泛保守基因的古老起源,这构成了“简单”的案例。对于不太稳健的情况,我们计算了一个基于随机化的经验P值,估计观察到的现存阅读框和祖先阅读框之间的保守性是否可以归因于偶然性.这个正式的标准使我们能够为大多数不太可靠的案例确定一个起源分支,鉴定了自酵母属分裂以来可以明确认为从头起源的49个基因,包括37个酿酒酵母特异性基因。我们发现,对于其余的模棱两可的情况,我们不能排除不同的进化场景,包括快速进化和多重损失,或最近的从头起源。总的来说,我们的研究结果表明,ASR是研究从头基因出现的一个有价值的工具,但应谨慎应用,并意识到其局限性.
New protein-coding genes can evolve from previously noncoding genomic regions through a process known as de novo gene emergence. Evidence suggests that this process has likely occurred throughout evolution and across the tree of life. Yet, confidently identifying de novo emerged genes remains challenging. Ancestral sequence reconstruction is a promising approach for inferring whether a gene has emerged de novo or not, as it allows us to inspect whether a given genomic locus ancestrally harbored protein-coding capacity. However, the use of ancestral sequence reconstruction in the context of de novo emergence is still in its infancy and its capabilities, limitations, and overall potential are largely unknown. Notably, it is difficult to formally evaluate the protein-coding capacity of ancestral sequences, particularly when new gene candidates are short. How well-suited is ancestral sequence reconstruction as a tool for the detection and study of de novo genes? Here, we address this question by designing an ancestral sequence reconstruction workflow incorporating different tools and sets of parameters and by introducing a formal criterion that allows to estimate, within a desired level of confidence, when protein-coding capacity originated at a particular locus. Applying this workflow on ∼2,600 short, annotated budding yeast genes (<1,000 nucleotides), we found that ancestral sequence reconstruction robustly predicts an ancient origin for the most widely conserved genes, which constitute \"easy\" cases. For less robust cases, we calculated a randomization-based empirical P-value estimating whether the observed conservation between the extant and ancestral reading frame could be attributed to chance. This formal criterion allowed us to pinpoint a branch of origin for most of the less robust cases, identifying 49 genes that can unequivocally be considered de novo originated since the split of the Saccharomyces genus, including 37 Saccharomyces cerevisiae-specific genes. We find that for the remaining equivocal cases we cannot rule out different evolutionary scenarios including rapid evolution, multiple gene losses, or a recent de novo origin. Overall, our findings suggest that ancestral sequence reconstruction is a valuable tool to study de novo gene emergence but should be applied with caution and awareness of its limitations.