Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.

中文翻译：

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果蝇亚群中只有一个分类学限制基因家族可以被高度可信地识别。

分类学限制基因（TRG）是仅存在于一个进化枝中的基因。蛋白质编码 TRG 可能从以前的非编码序列从头进化而来：功能性 ncRNA、内含子或旧蛋白质编码基因的替代阅读框或基因间序列。研究从头基因的一个主要挑战是需要避免假阳性（非功能性开放阅读框和/或不是从头出现的功能基因）和假阴性。在这里，我们保守地寻找高置信度的 TRG 作为最有希望进行实验研究的候选者，通过至少两个物种的保护来确保功能，并通过检查同源非编码序列来确保从头状态。我们的管道还避免了与从头基因如何诞生的先入之见相关的确定偏差。我们确定了一个在果蝇亚群中从头进化的 TRG 家族。该 TRG 家族在模拟果蝇 (Drosophila simulans)和果蝇 (Drosophila sechellia)中含有单拷贝基因。它起源于一个成熟基因的内含子，与上游另一个成熟基因共享该内含子。这些 TRG 包含早于其开放阅读框的内含子。这些基因此前并未被报道为从头起源，据我们所知，它们是迄今为止为阐明从头基因特性的实验研究确定的最佳果蝇候选基因。