Zhang Xiaojun, Sun Lina, Yuan Jianbo, Sun Yamin, Gao Yi, Zhang Libin, Li Shihao, Dai Hui, Hamel Jean-François, Liu Chengzhang, Yu Yang, Liu Shilin, Lin Wenchao, Guo Kaimin, Jin Songjun, Xu Peng, Storey Kenneth B, Huan Pin, Zhang Tao, Zhou Yi, Zhang Jiquan, Lin Chenggang, Li Xiaoni, Xing Lili, Huo Da, Sun Mingzhe, Wang Lei, Mercier Annie, Li Fuhua, Yang Hongsheng, Xiang Jianhai
Key Laboratory of Experimental Marine Biology & Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
Laboratory for Marine Biology and Biotechnology & Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
PLoS Biol. 2017 Oct 12;15(10):e2003790. doi: 10.1371/journal.pbio.2003790. eCollection 2017 Oct.
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.
除了与脊索动物有着共同的祖先外，海参还具有独特的形态和非凡的再生能力。在此，我们展示了一种经济上重要的海参——日本刺参的完整基因组序列，该序列是使用Illumina和PacBio平台生成的，组装大小约为805 Mb（重叠群N50为190 Kb，支架N50为486 Kb），含有30350个蛋白质编码基因且连续性高。我们利用这一资源探索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鳃裂相关的标记基因的存在，这表明这些脊索动物特征存在于棘皮动物的祖先中。海参成体独特的形状和较弱的矿化作用也通过生物矿化基因的收缩得到了初步解释。对诱导排脏后器官再生的基因组、转录组和蛋白质组分析，为内脏再生的分子基础提供了见解，包括一个特定的串联重复的94个氨基酸的前列腺分泌蛋白（PSP94）样基因家族和一个显著扩增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研究后口动物的生物过程和进化提供有用的框架，包括可能具有医学应用价值的显著再生能力。此外，多组学数据对商业海参育种计划具有重要价值。
