不同物种的Y染色体融合进化出基因贫乏,富含重复基因的异色组织,LTR反转录转座子,卫星DNA性拮抗和重组的丧失在年轻Y染色体的变性中起主要作用。然而,塑造成熟进化的过程,已经退化的Y染色体不太清楚。因为Y染色体进化得很快,密切相关的物种之间的比较是特别有用的。我们生成了从头长阅读组件,并辅以细胞学验证,以揭示果蝇模拟复合体的三个密切相关物种中的Y染色体组织,它仅在25万年前分离,并共享>98%的序列同一性。我们发现这些Y染色体在其组织和重复DNA组成上是不同的,并发现了新的Y连锁基因家族,其进化是由正选择和基因转换驱动的。这些Y染色体也富含大量缺失,表明Y染色体上双链断裂的修复可能偏向于微同源性介导的末端连接,而不是经典的非同源末端连接。我们认为这种修复机制有助于跨生物体的Y染色体组织的趋同进化。
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long-read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.