Data from: High rate of translocation-based gene birth on the Drosophila Y chromosome

The Y chromosome is a unique genetic environment defined by a lack of recombination and male-limited inheritance. The Drosophila Y chromosome has been gradually acquiring genes from the rest of the genome, with only seven Y-linked genes being gained over the past 63 million years (0.12 gene gains per million years). Using a next-generation sequencing (NGS)-powered genomic scan, we show that gene transfers to the Y chromosome are much more common than previously suspected: at least 25 have arisen across three Drosophila species over the past 5.4 million years (1.67 per million years for each lineage). The gene transfer rate is significantly lower in Drosophila melanogaster than in the Drosophila simulans clade, primarily due to Y-linked retrotranspositions being significantly more common in the latter. Despite all Y-linked gene transfers being evolutionarily recent (<1 million years old), only three showed evidence for purifying selection (ω ≤ 0.14). Thus, although the resulting Y-linked functional gene acquisition rate (0.25 new genes per million years) is double the longer-term estimate, the fate of most new Y-linked genes is defined by rapid degeneration and pseudogenization. Our results show that Y-linked gene traffic, and the molecular mechanisms governing these transfers, can diverge rapidly between species, revealing the Drosophila Y chromosome to be more dynamic than previously appreciated. Our analytical method provides a powerful means to identify Y-linked gene transfers and will help illuminate the evolutionary dynamics of the Y chromosome in Drosophila and other species.Y染色体是一类独特的遗传环境，其特征为缺乏重组且遵循限雄遗传模式。果蝇属（Drosophila）的Y染色体一直在从基因组其他区域逐步获取基因，过去6300万年中仅获得了7个Y连锁基因，平均每百万年新增0.12个基因。本研究借助下一代测序（next-generation sequencing，NGS）驱动的全基因组扫描分析，发现向Y染色体的基因转移事件远比此前预想的更为频繁：在过去540万年中，3个果蝇物种的基因组中至少已出现25次此类转移事件，每个支系的转移速率为每百万年1.67次。黑腹果蝇（Drosophila melanogaster）的基因转移速率显著低于拟暗果蝇支系（Drosophila simulans clade），这主要是因为后者的Y连锁逆转座事件更为普遍。尽管所有Y连锁基因转移事件在进化上都属于新近发生（距今不足100万年），但其中仅有3个显示出净化选择的证据（ω ≤ 0.14）。因此，尽管由此得到的Y连锁功能性基因获取速率（每百万年0.25个新基因）是长期估算值的两倍，但大多数新获得的Y连锁基因最终都会快速退化并发生假基因化。本研究结果表明，Y连锁基因流以及调控这些转移事件的分子机制，在不同物种间可快速分化，这揭示出果蝇Y染色体的动态性远超此前认知。本研究的分析方法为鉴定Y连锁基因转移事件提供了高效手段，将有助于阐明果蝇及其他物种Y染色体的进化动态。