Satellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here, we use high-quality genome assemblies to study the evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 g/cm³, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spread by inserting into existing clusters of the older, more abundant 1.688 satellite, in events likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.

中文翻译：

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果蝇和模拟进化枝 X 染色体常色卫星的动态演化。


卫星 DNA (satDNA) 是真核基因组中进化最动态的组成部分之一，在基因组调控、基因组进化和物种形成中发挥着重要作用。尽管其丰富性和功能影响，我们对塑造基因组中 satDNA 分布的进化动力学和分子机制知之甚少。在这里，我们使用高质量的基因组组装来研究果蝇及其在模拟分支中的三个最近亲缘关系中的两种复杂 satDNA（ Rsp-like和1.688 g/cm ^{3 ）}的进化动力学。我们发现，这些重复的大块在异染色质中是高度动态的，它们的基因组位置因物种而异。我们发现，X 染色体常染色质中丰富的 satDNA 小块也具有类似的动态性，不同物种之间重复序列的丰度、位置和组成都发生变化。我们详细描述了D. simulans和D. mauritiana中罕见卫星（ Rsp 样）在 X 染色体上的增殖。通过插入更古老、更丰富的1.688卫星的现有星团来进行类似 Rsp 的传播，这可能是由微同源介导的修复途径促进的事件。我们发现，模拟拟果蝇的染色体外环状 DNA 上富含Rsp-like ，这可能有助于其动态进化。位点内 satDNA 通过不等交换的扩展和高阶重复的移动也有助于重复景观的流动性。 我们发现证据表明，常染色质 satDNA 重复经历了增殖和多样化的循环，这在某种程度上类似于转座元件增殖的爆发。我们的研究为 satDNA 增殖的机制研究以及 satDNA 运动的功能和进化后果奠定了基础。