Gebert Daniel, Hay Amir D, Hoang Jennifer P, Gibbon Adam E, Henderson Ian R, Teixeira Felipe Karam
Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
Genome Biol. 2025 Mar 18;26(1):63. doi: 10.1186/s13059-025-03527-4.
The Drosophila genus is ideal for studying genome evolution due to its relatively simple chromosome structure and small genome size, with rearrangements mainly restricted to within chromosome arms, such as Muller elements. However, work on the rapidly evolving repetitive genomic regions, composed of transposons and tandem repeats, have been hampered by the lack of genus-wide chromosome-level assemblies.
Integrating long-read genomic sequencing and chromosome capture technology, here we produce and annotate 30 chromosome-level genome assemblies within the Drosophila genus. Based on this dataset, we reveal the evolutionary dynamics of genome rearrangements across the Drosophila phylogeny, including the identification of genomic regions that show comparatively high structural stability throughout evolution. Moreover, within the ananassae subgroup, we uncover the emergence of new chromosome conformations and the rapid expansion of novel satellite DNA sequence families, which form large and continuous pericentromeric domains with higher-order repeat structures that are reminiscent of those observed in the human and Arabidopsis genomes.
These chromosome-level genome assemblies present a valuable resource for future research, the power of which is demonstrated by our analysis of genome rearrangements and chromosome evolution. In addition, based on our findings, we propose the ananassae subgroup as an ideal model system for studying the evolution of centromere structure.
果蝇属因其相对简单的染色体结构和较小的基因组大小，是研究基因组进化的理想对象，其重排主要局限于染色体臂内，如穆勒元件。然而，由转座子和串联重复组成的快速进化的重复基因组区域的研究，因缺乏全属范围的染色体水平组装而受到阻碍。
整合长读长基因组测序和染色体捕获技术，我们在此生成并注释了果蝇属内30个染色体水平的基因组组装。基于该数据集，我们揭示了果蝇系统发育中基因组重排的进化动态，包括鉴定出在整个进化过程中显示出较高结构稳定性的基因组区域。此外，在拟果蝇亚组中，我们发现了新的染色体构象的出现以及新的卫星DNA序列家族的快速扩张，这些家族形成了具有高阶重复结构的大的连续着丝粒周围区域，让人联想到在人类和拟南芥基因组中观察到的那些区域。
这些染色体水平的基因组组装为未来研究提供了宝贵资源，我们对基因组重排和染色体进化的分析证明了其作用。此外，基于我们的发现，我们提出拟果蝇亚组是研究着丝粒结构进化的理想模型系统。
