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Genome-wide analysis of gene expression profile in the respiratory tree of sea cucumber (Apostichopus japonicus) in response to hypoxia conditions

Published online by Cambridge University Press:  13 September 2017

Libin Zhang Open the ORCID record for Libin Zhang [Opens in a new window] ,
Qiming Feng ,
Kui Ding ,
Lina Sun ,
Da Huo ,
Yan Fang ,
Tao Zhang  and
Hongsheng Yang
Libin Zhang
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
Qiming Feng
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China University of Chinese Academy of Sciences, 19A Yuquan Rd, Shijingshan District, Beijing 100049, China
Kui Ding
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China University of Chinese Academy of Sciences, 19A Yuquan Rd, Shijingshan District, Beijing 100049, China
Lina Sun
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
Da Huo
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China University of Chinese Academy of Sciences, 19A Yuquan Rd, Shijingshan District, Beijing 100049, China
Yan Fang
Affiliation:
School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
Tao Zhang
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
Hongsheng Yang*
Affiliation:
CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
*
Correspondence should be addressed to: H. Yang CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China email: [email protected]
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Abstract

The sea cucumber Apostichopus japonicus is a deposit-feeder and vital for marine benthic ecosystems. Hypoxia can influence the behaviour and even lead to massive mortality in A. japonicus in the wild. It is important to understand the molecular responses of A. japonicus when exposed to acute changes in dissolved oxygen (DO) concentration. In this study, RNA-seq provided a general overview of the gene expression profiles of the respiratory tree of A. japonicus exposed to DO of 8 mg l−1 (DO8), 4 mg l−1 (DO4) and 2 mg l−1 (DO2) conditions. Differentially expressed genes (DEGs) screening with the NOISeq method identified 51, 59 and 61 DEGs according to the criteria of fold change ≥2 and divergence probability ≥0.8 in the comparisons of DO2 vs DO4, DO2 vs DO8 and DO4 vs DO8, respectively. Gene ontology analysis showed that ‘cellular process’ and ‘binding’ had the most enriched DEGs in the categories of ‘biological process’ and ‘molecular function’, respectively (catalytic activity also had the most enriched DEGs in the category of ‘molecular function’ based on the comparison of DO2 vs DO8), while ‘cell’ and ‘cell part’ had the most enriched DEGs in the category of ‘cellular component’. The DEGs were mapped to 79, 81 and 104 pathways in the KEGG database, and 8, 29 and 16 pathways were significantly enriched, respectively. The DO-specific DEGs identified in this study of the respiratory tree are important targets for further research into the biochemical mechanisms involved in the response of the sea cucumber to changes in the DO concentration.

Keywords

Apostichopus japonicusrespiratory treehypoxiastress responsemetabolic pathway
Type
Research Article
Information
Journal of the Marine Biological Association of the United Kingdom , Volume 98 , Special Issue 8: Special Section: European Marine Biology Symposium Papers 2018 , December 2018 , pp. 2039 - 2048
Copyright
Copyright © Marine Biological Association of the United Kingdom 2017 

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