The sea cucumber genome provides insights into morphological evolution and visceral regeneration.
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 assem...
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-10-01
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| Series: | PLoS Biology |
| Online Access: | https://doi.org/10.1371/journal.pbio.2003790 |
| _version_ | 1819124387589128192 |
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| author | Xiaojun Zhang Lina Sun Jianbo Yuan Yamin Sun Yi Gao Libin Zhang Shihao Li Hui Dai Jean-François Hamel Chengzhang Liu Yang Yu Shilin Liu Wenchao Lin Kaimin Guo Songjun Jin Peng Xu Kenneth B Storey Pin Huan Tao Zhang Yi Zhou Jiquan Zhang Chenggang Lin Xiaoni Li Lili Xing Da Huo Mingzhe Sun Lei Wang Annie Mercier Fuhua Li Hongsheng Yang Jianhai Xiang |
| author_facet | Xiaojun Zhang Lina Sun Jianbo Yuan Yamin Sun Yi Gao Libin Zhang Shihao Li Hui Dai Jean-François Hamel Chengzhang Liu Yang Yu Shilin Liu Wenchao Lin Kaimin Guo Songjun Jin Peng Xu Kenneth B Storey Pin Huan Tao Zhang Yi Zhou Jiquan Zhang Chenggang Lin Xiaoni Li Lili Xing Da Huo Mingzhe Sun Lei Wang Annie Mercier Fuhua Li Hongsheng Yang Jianhai Xiang |
| author_sort | Xiaojun Zhang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T07:23:26Z |
| format | Article |
| id | doaj.art-48a1eec76ee24f74bc33889df620b1a8 |
| institution | Directory Open Access Journal |
| issn | 1544-9173 1545-7885 |
| language | English |
| last_indexed | 2024-12-22T07:23:26Z |
| publishDate | 2017-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj.art-48a1eec76ee24f74bc33889df620b1a82022-12-21T18:34:13ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852017-10-011510e200379010.1371/journal.pbio.2003790The sea cucumber genome provides insights into morphological evolution and visceral regeneration.Xiaojun ZhangLina SunJianbo YuanYamin SunYi GaoLibin ZhangShihao LiHui DaiJean-François HamelChengzhang LiuYang YuShilin LiuWenchao LinKaimin GuoSongjun JinPeng XuKenneth B StoreyPin HuanTao ZhangYi ZhouJiquan ZhangChenggang LinXiaoni LiLili XingDa HuoMingzhe SunLei WangAnnie MercierFuhua LiHongsheng YangJianhai XiangApart 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.https://doi.org/10.1371/journal.pbio.2003790 |
| spellingShingle | Xiaojun Zhang Lina Sun Jianbo Yuan Yamin Sun Yi Gao Libin Zhang Shihao Li Hui Dai Jean-François Hamel Chengzhang Liu Yang Yu Shilin Liu Wenchao Lin Kaimin Guo Songjun Jin Peng Xu Kenneth B Storey Pin Huan Tao Zhang Yi Zhou Jiquan Zhang Chenggang Lin Xiaoni Li Lili Xing Da Huo Mingzhe Sun Lei Wang Annie Mercier Fuhua Li Hongsheng Yang Jianhai Xiang The sea cucumber genome provides insights into morphological evolution and visceral regeneration. PLoS Biology |
| title | The sea cucumber genome provides insights into morphological evolution and visceral regeneration. |
| title_full | The sea cucumber genome provides insights into morphological evolution and visceral regeneration. |
| title_fullStr | The sea cucumber genome provides insights into morphological evolution and visceral regeneration. |
| title_full_unstemmed | The sea cucumber genome provides insights into morphological evolution and visceral regeneration. |
| title_short | The sea cucumber genome provides insights into morphological evolution and visceral regeneration. |
| title_sort | sea cucumber genome provides insights into morphological evolution and visceral regeneration |
| url | https://doi.org/10.1371/journal.pbio.2003790 |
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