Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

几乎所有现存动物谱系中的物种都能够再生身体部位。然而，目前尚不清楚控制再生的基因表达程序在进化上是否保守。海蛇尾是一类物种丰富的棘皮动物，具有出色的再生能力，但由于基因组资源有限，对该类动物再生遗传基础的研究受到阻碍。在这里，我们报告了海蛇尾Amphiura filiformis的染色体规模基因组组装。我们发现，海蛇尾基因组是迄今为止测序的棘皮动物中重排最严重的，其特征是重组的 Hox 簇，让人想起在海胆中观察到的重排。此外，我们对海蛇尾成年臂再生过程中的基因表达进行了广泛的分析，并确定了控制伤口愈合、增殖和分化的基因表达的连续波。我们与其他无脊椎动物和脊椎动物模型进行了附肢再生的比较转录组分析，发现了数百个具有保守表达动态的基因，特别是在再生的增殖阶段。我们的研究结果强调了棘皮动物对于检测脊椎动物和经典无脊椎动物再生模型系统之间的远程表达保守性的至关重要性。