Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

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...

跨多样物种的Y染色体趋同演化出基因贫乏的异染色质组织结构，该结构富集重复基因、长末端重复序列逆转录转座子（LTR retrotransposons）与卫星DNA。性拮抗与重组丧失在年轻Y染色体的退化过程中发挥核心作用。然而，针对成熟且已发生退化的Y染色体的进化塑造机制，目前学界的认知仍相对有限。由于Y染色体进化速率较快，近缘物种间的比较分析具备尤为重要的研究价值。我们通过长读长从头组装（de novo long read assemblies）结合细胞学验证（cytological validation），解析了拟果蝇复合种（Drosophila simulans complex）中3个近缘物种的Y染色体组织结构；这些物种的分化时间仅为25万年，序列一致性超过98%。我们发现这些Y染色体在组织结构与重复DNA组成上存在显著分化，并鉴定出全新的Y连锁基因家族，其演化受到正选择（positive selection）与基因转换（gene conversion）的共同驱动。这些Y染色体同时还……