| Transcriptomic analysis reveals insights into deep-sea adaptations of the dominant species, Shinkaia crosnieri (Crustacea: Decapoda: Anomura), inhabiting both hydrothermal vents and cold seeps | |
Cheng, Jiao1,3; Hui, Min1,3; Sha, Zhongli1,2,3,4
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| 2019-05-18 | |
| Source Publication | BMC GENOMICS
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| ISSN | 1471-2164 |
| Volume | 20Pages:16 |
| Corresponding Author | Sha, Zhongli(shazl@qdio.ac.cn) |
| Abstract | BackgroundHydrothermal vents and cold seeps are typical deep-sea chemosynthetically-driven ecosystems that allow high abundance of specialized macro-benthos. To gather knowledge about the genetic basis of adaptation to these extreme environments, species shared between different habitats, especially for the dominant species, are of particular interest. The galatheid squat lobster, Shinkaia crosnieri Baba and Williams, 1998, is one of the few dominant species inhabiting both deep-sea hydrothermal vents and cold seeps. In this study, we performed transcriptome analyses of S. crosnieri collected from the Iheya North hydrothermal vent (HV) and a cold seep in the South China Sea (CS) to provide insights into how this species has evolved to thrive in different deep-sea chemosynthetic ecosystems.ResultsWe analyzed 5347 orthologs between HV and CS to identify genes under positive selection through the maximum likelihood approach. A total of 82 genes were identified to be positively selected and covered diverse functional categories, potentially indicating their importance for S. crosnieri to cope with environmental heterogeneity between deep-sea vents and seeps. Among 39,806 annotated unigenes, a large number of differentially expressed genes (DEGs) were identified between HV and CS, including 339 and 206 genes significantly up-regulated in HV and CS, respectively. Most of the DEGs associated with stress response and immunity were up-regulated in HV, possibly allowing S. crosnieri to increase its capability to manage more environmental stresses in the hydrothermal vents.ConclusionsWe provide the first comprehensive transcriptomic resource for the deep-sea squat lobster, S. crosnieri, inhabiting both hydrothermal vents and cold seeps. A number of stress response and immune-related genes were positively selected and/or differentially expressed, potentially indicating their important roles for S. crosnieri to thrive in both deep-sea vents and cold seeps. Our results indicated that genetic adaptation of S. crosnieri to different deep-sea chemosynthetic environments might be mediated by adaptive evolution of functional genes related to stress response and immunity, and alterations in their gene expression that lead to different stress resistance. However, further work is required to test these proposed hypotheses. All results can constitute important baseline data for further studies towards elucidating the adaptive mechanisms in deep-sea crustaceans. |
| Keyword | Galatheidae Deep-sea adaptation Comparative transcriptome Positive selection Differential expression |
| DOI | 10.1186/s12864-019-5753-7 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | National Key R&D Program of China[2018YFC0310702] ; National Key R&D Program of China[2018YFC0310802] ; National Natural Science Foundation of China[31872215] ; Key Research Program of Frontier Sciences of Chinese Academy of Sciences[QYZDB-SSW-DQC036] ; Senior User Project of RV KEXUE[KEXUE2018G21] ; National Key R&D Program of China[2018YFC0310702] ; National Key R&D Program of China[2018YFC0310802] ; National Natural Science Foundation of China[31872215] ; Key Research Program of Frontier Sciences of Chinese Academy of Sciences[QYZDB-SSW-DQC036] ; Senior User Project of RV KEXUE[KEXUE2018G21] |
| WOS Research Area | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS Subject | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS ID | WOS:000468169200001 |
| Publisher | BMC |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.qdio.ac.cn/handle/337002/161422 |
| Collection | 海洋生物分类与系统演化实验室 |
| Corresponding Author | Sha, Zhongli |
| Affiliation | 1.Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao 266071, Shandong, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Shandong, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Shandong, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| First Author Affilication | Institute of Oceanology, Chinese Academy of Sciences; Center for Ocean Mega-Science, Chinese Academy of Sciences |
| Corresponding Author Affilication | Institute of Oceanology, Chinese Academy of Sciences; Center for Ocean Mega-Science, Chinese Academy of Sciences |
| Recommended Citation GB/T 7714 | Cheng, Jiao,Hui, Min,Sha, Zhongli. Transcriptomic analysis reveals insights into deep-sea adaptations of the dominant species, Shinkaia crosnieri (Crustacea: Decapoda: Anomura), inhabiting both hydrothermal vents and cold seeps[J]. BMC GENOMICS,2019,20:16. |
| APA | Cheng, Jiao,Hui, Min,&Sha, Zhongli.(2019).Transcriptomic analysis reveals insights into deep-sea adaptations of the dominant species, Shinkaia crosnieri (Crustacea: Decapoda: Anomura), inhabiting both hydrothermal vents and cold seeps.BMC GENOMICS,20,16. |
| MLA | Cheng, Jiao,et al."Transcriptomic analysis reveals insights into deep-sea adaptations of the dominant species, Shinkaia crosnieri (Crustacea: Decapoda: Anomura), inhabiting both hydrothermal vents and cold seeps".BMC GENOMICS 20(2019):16. |
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| Transcriptomic analy（3691KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View | |
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