Supporting data for "The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses"

The ability of octocorals and stony corals to deposit calcium carbonate (CaCO₃) has contributed to their ecological success. While stony corals possess a homogeneous aragonite skeleton, octocorals have developed distinct skeletal structures composed of different CaCO₃ polymorphs and skeletal organic matrix. Nevertheless, the molecular basis of skeletal structure formation in octocorals remains inadequately understood. <br>Here, we sequenced the genomes and skeletal proteomes of two calcite-forming octocorals, namely <i>Paragorgia papillata</i> and <i>Chrysogorgia sp.</i> The assembled genomes sizes were 618.13 Mb and 781.04 Mb for <i>P. papillata</i> and <i>Chrysogorgia sp.</i>, respectively, with contig N50 of 2.67 Mb and 2.61 Mb. Comparative genomic analyses identified 162 and 285 significantly expanded gene families in the genomes of <i>P. papillata</i> and <i>Chrysogorgia sp.</i>, respectively, which are primarily associated with biomineralization and immune response. Furthermore, comparative analyses of skeletal proteomes demonstrated that corals with different CaCO₃ polymorphs share a fundamental toolkit comprising cadherin, von Willebrand factor type A, and carbonic anhydrase domains for calcified skeleton deposition. In contrast, collagen is rich in the calcite-forming octocoral skeletons but occurs rarely in aragonitic stony corals. Additionally, certain collagens have developed domains related to matrix adhesion and immunity, which may confer novel genetic functions in octocoral calcification. <br>These findings enhance our understanding of the diverse forms of coral biomineralization processes and offer preliminary insights into the formation and evolution of the octocoral skeleton.

八放珊瑚与石珊瑚沉积碳酸钙（CaCO₃）的能力，助力二者在生态系统中取得成功。石珊瑚拥有均质的文石骨架，而八放珊瑚则演化出由不同碳酸钙（CaCO₃）晶型及骨骼有机基质构成的独特骨骼结构。然而，当前学界对八放珊瑚骨骼结构形成的分子基础仍知之甚少。

本研究对两种形成方解石的八放珊瑚——帕氏拟柳珊瑚（*Paragorgia papillata*）与金柳珊瑚未定种（*Chrysogorgia* sp.）的基因组及骨骼蛋白质组进行了测序。帕氏拟柳珊瑚与金柳珊瑚未定种的组装基因组大小分别为618.13 Mb与781.04 Mb，重叠群N50分别为2.67 Mb与2.61 Mb。比较基因组分析显示，帕氏拟柳珊瑚与金柳珊瑚未定种的基因组中分别存在162个和285个显著扩张的基因家族，这些家族主要与生物矿化及免疫应答相关。此外，骨骼蛋白质组比较分析表明，携带不同碳酸钙晶型的珊瑚共享一套核心钙化骨架沉积工具包，该工具包包含钙粘蛋白（cadherin）、血管性血友病因子A域（von Willebrand factor type A）以及碳酸酐酶（carbonic anhydrase）结构域。与之相对，胶原蛋白在形成方解石的八放珊瑚骨骼中含量丰富，但在文石质石珊瑚骨架中极为罕见。另有部分胶原蛋白演化出与基质黏附和免疫相关的结构域，这可能为八放珊瑚的钙化过程赋予了全新的遗传功能。

上述发现加深了我们对珊瑚生物矿化过程多样性的理解，并为八放珊瑚骨骼的形成与演化提供了初步研究视角。