The planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.

涡虫Schmidtea mediterranea正在作为再生模型物种进行研究，但涡虫基因组的组装仍然具有挑战性。在这里，我们报告了地中海链球菌有性 S2 菌株的高质量单倍型定相、染色体规模基因组组装，以及其三个近亲S. polychroa 、 S. nova和S. nova的高质量染色体规模组装。 . 卢古布里斯.使用混合基因注释和优化的 ATAC-seq 和 ChIP-seq 协议进行调控元件注释，我们为涡虫研究界提供了宝贵的基因组资源，并为涡虫基因组进化提供了第一个比较视角。我们的分析揭示了蛋白质编码序列和调控区域存在显着差异，但启动子和增强子注释中存在相当大的保守性。我们还发现Schmidtea属内频繁发生与逆转录转座子相关的染色体倒位和染色体间易位，并且值得注意的是， Schmidtea和其他两个扁虫类群的祖先后生动物同线性独立且几乎完全丧失。总的来说，我们的结果表明扁形动物基因组可以在没有同线性限制的情况下进化。