Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

海参除了具有与脊索动物相同的祖先外，还表现出独特的形态和出色的再生能力。在这里，我们介绍了经济上重要的海参A的完整基因组序列。日本，使用Illumina和PacBio平台生成，可实现约805 Mb的装配（190 Kb的重叠群N50和486 Kb的脚手架N50），以及30,350个蛋白质编码基因，并具有高度连续性。我们利用这一资源探索了海参独特生物学特性背后的关键遗传机制。系统发育和比较基因组分析揭示了与脊索和and裂相关的标记基因的存在，表明这些cho酸盐特征存在于祖先棘皮动物中。还通过生物矿化基因的收缩初步解释了海参成虫的独特形状和微弱的矿化作用。诱导内脏去除后器官再生的基因组，转录组和蛋白质组分析提供了对内脏再生的分子基础的见解，包括一个特定的串联复制的94个氨基酸的前列腺分泌蛋白（PSP94）样基因家族和一个显着扩展的纤维蛋白原相关蛋白（FREP）基因家族。这种高质量的基因组资源将为未来的氘化口琴的生物学过程和进化研究提供有用的框架，包括可在医学上应用的显着的再生能力。此外，多组学数据对于商业海参育种计划将具有重要价值。包括非凡的再生能力，可能具有医疗应用。此外，多组学数据对于商业海参育种计划将具有重要价值。包括非凡的再生能力，可能具有医疗应用。此外，多组学数据对于商业海参育种计划将具有重要价值。