Department of Biology, University of Rochester, Rochester, United States.
School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, United States.
Elife. 2022 Jan 6;11:e75795. doi: 10.7554/eLife.75795.
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 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.
Y 染色体在不同物种中趋同进化为基因贫乏、异染色质组织，富含重复基因、长末端重复转座子和卫星 DNA。性拮抗和重组的丧失在年轻 Y 染色体的退化中起着主要作用。然而，塑造成熟、已经退化的 Y 染色体进化的过程还不太清楚。由于 Y 染色体进化迅速，因此密切相关的物种之间的比较特别有用。我们生成了从头开始的长读组装，并辅以细胞学验证，以揭示复杂的三个密切相关物种中的 Y 染色体组织，它们仅在 25 万年前分化，并且共享 >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 组成上存在差异，并发现了新的 Y 连锁基因家族，其进化受到正选择和基因转换的驱动。这些 Y 染色体也富含大片段缺失，表明 Y 染色体双链断裂的修复可能偏向于微同源介导的末端连接，而不是经典的非同源末端连接。我们提出，这种修复机制有助于生物体中 Y 染色体组织的趋同进化。
