Data from: The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive

Background: Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster. Rsp is well-known for being the target of Segregation Distorter (SD) an autosomal meiotic drive system in D. melanogaster. I present an evolutionary genetic analysis of the Rsp family of repeats in D. melanogaster and its closely-related species in the melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta, and D. yakuba) using a combination of available BAC sequences, whole genome shotgun Sanger reads, Illumina short read deep sequencing, and fluorescence in situ hybridization. Results: I show that Rsp repeats have euchromatic locations throughout the D. melanogaster genome, that Rsp arrays show evidence for concerted evolution, and that Rsp repeats exist outside of D. melanogaster, in the melanogaster group. The repeats in these species are considerably diverged at the sequence level compared to D. melanogaster, and have a strikingly different genomic distribution, even between closely-related sister taxa. Conclusions: The genomic organization of the Rsp repeat in the D. melanogaster genome is complex--it exists of large blocks of tandem repeats in the heterochromatin and small blocks of tandem repeats in the euchromatin. My discovery of heterochromatic Rsp-like sequences outside of D. melanogaster suggests that SD evolved after its target satellite and that the evolution of the Rsp satellite family is highly dynamic over a short evolutionary time scale (<240,000 years).

**背景**：卫星DNA（Satellite DNA）可占真核生物基因组的相当大比例，在基因组结构构建与染色体分离过程中发挥重要功能。卫星DNA的快速进化可引发基因组不稳定性，并导致物种间遗传不相容性。尽管卫星DNA分布广泛且对基因组演化具有重要贡献，但目前学界对其进化动态的认知仍较为有限。Responder（Rsp）卫星DNA家族定位于黑腹果蝇（Drosophila melanogaster）2号染色体的着丝粒周边异染色质区域，该家族作为黑腹果蝇中常染色体减数分裂驱动系统——分离畸变（Segregation Distorter, SD）的靶标序列而广为人知。本研究结合现有细菌人工染色体（Bacterial Artificial Chromosome, BAC）序列、全基因组鸟枪法Sanger测序读段、Illumina短读长深度测序数据与荧光原位杂交（Fluorescence In Situ Hybridization, FISH）技术，对黑腹果蝇及其黑腹果蝇组近缘物种（拟果蝇D. simulans、塞舌尔果蝇D. sechellia、毛里求斯果蝇D. mauritiana、直立果蝇D. erecta及雅库巴果蝇D. yakuba）开展进化遗传学分析。

**结果**：本研究证实，Rsp重复序列在黑腹果蝇全基因组中均存在常染色质定位；Rsp重复阵列呈现协同进化的分子特征；且在黑腹果蝇组的其他物种中同样存在Rsp同源重复序列。相较于黑腹果蝇，这些物种中的Rsp重复序列在序列水平上已发生显著分化，且即使在亲缘关系极近的姊妹类群之间，其基因组分布模式也存在显著差异。

**结论**：黑腹果蝇基因组中Rsp重复序列的基因组组织形式较为复杂——其在异染色质区域以大片段串联重复形式存在，而在常染色质区域则以小片段串联重复形式分布。本研究在黑腹果蝇以外的物种中发现了异染色质定位的类Rsp序列，这表明分离畸变系统（SD）是在其靶标卫星DNA演化之后才出现的；同时也说明Rsp卫星DNA家族在短至<24万年的进化时间尺度内，呈现出高度动态的演化特征。