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PLoS Biol. 2017 Oct 12;15(10):e2003790. doi: 10.1371/journal.pbio.2003790. eCollection 2017 Oct.

The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

Zhang X1,2, Sun L1,2, Yuan J1,2, Sun Y3, Gao Y1,2, Zhang L1,2, Li S1,2, Dai H3, Hamel JF4, Liu C1,2, Yu Y1,2, Liu S1,2, Lin W3, Guo K3, Jin S1,2, Xu P5, Storey KB6, Huan P1,2, Zhang T1,2, Zhou Y1,2, Zhang J1,2, Lin C1,2, Li X1,7, Xing L1,7, Huo D1,7, Sun M1,7, Wang L8, Mercier A9, Li F1,2, Yang H1,2, Xiang J1,2.

Author information

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.
Tianjin Biochip Corporation, Tianjin, China.
Society for the Exploration and Valuing of the Environment (SEVE), Portugal Cove-St. Philips, Newfoundland, Canada.
College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
Department of Biology, Carleton University, Ottawa, Ontario, Canada.
University of Chinese Academy of Sciences, Beijing, China.
College of Life Sciences, Nankai University, Tianjin, China.
Department of Ocean Sciences, Memorial University, St. John's, Newfoundland, Canada.


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.

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