The genome of Aphrocallistes vastus. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization

Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genome resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is ~80 MB, small compared to most other metazoans, and contains nearly 2,500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO2), and we identified 419 differentially expressed genes between the osculum, i.e., the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes, such as collagens, actins, and glassin, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO2 deposition in the Silicea sensu stricto (Hexactinellida+Demospongiae) may not be homologous.

注释完善且连续完整的基因组，是解析生物演化、发育与代谢能力不可或缺的核心资源。海绵作为一类在生态系统中具有重要地位的非两侧对称动物类群，多为滤食性固着水生生物，但其现有基因组资源的覆盖度仍远低于预期。本研究报道了大疣六放海绵（Aphrocallistes vastus）的高质量注释基因组，该物种属于玻璃海绵（多孔动物门：六放海绵纲（Hexactinellida）），可在加拿大不列颠哥伦比亚省沿岸形成大型礁体。研究显示，该基因组大小约为80 Mb，相较于多数其他后生动物（Metazoa）基因组更为小巧，且包含近2500个嵌套基因，数量多于其他已发表的海绵基因组。六放海绵纲以无定形二氧化硅（SiO₂）构成的独特骨骼架构为典型特征；本研究鉴定出该海绵出水孔（即其垂直生长区域）与主体之间的419个差异表达基因。在上调表达的基因中，胶原蛋白（collagens）、肌动蛋白（actins）与玻璃蛋白（glassin）等矿化相关基因主导了其生长阶段的表达谱。过往研究认为硅蛋白（silicateins）参与二氧化硅矿化过程，尤其在寻常海绵纲（Demospongiae）中，但在A. vastus的基因组中完全未发现该基因；这一结果提示，狭义硅质海绵类群（Silicea sensu stricto，即六放海绵纲+寻常海绵纲）的SiO₂沉积潜在机制可能并非同源。