Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.

鹦鹉螺是古生代唯一幸存的有壳头足类动物。它在头足类动物谱系中是独一无二的，对于理解头足类动物的进化新颖性至关重要。在这里，我们展示了完整的鹦鹉螺基因组，作为头足类创新（例如针孔眼和生物矿化）的基本基因组参考。鹦鹉螺显示出紧凑、简约的基因组，编码基因很少，并且在已知的头足类动物中，非编码区和编码区的进化速度都很慢。重要的是，多种基因组创新，包括基因丢失、特定基因家族的独立收缩和扩张及其相关的调控网络，可能塑造了鹦鹉螺针孔眼的进化。保守的软体动物生物矿化工具包和谱系特异性重复低复杂性结构域对于鹦鹉螺壳的构建至关重要。鹦鹉螺基因组是重建塑造现存头足类动物的进化场景和基因组创新的宝贵资源。