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Zhong Z, Guo Y, Zhou L, Chen H, Lian C, Wang H, Zhang H, Cao L, Sun Y, Wang M, Li C. Transcriptomic responses and evolutionary insights of deep-sea and shallow-water mussels under high hydrostatic pressure condition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175185. [PMID: 39089385 DOI: 10.1016/j.scitotenv.2024.175185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Marine mussels inhabit a wide range of ocean depths, necessitating unique adaptations to cope with varying hydrostatic pressures. This study investigates the transcriptomic responses and evolutionary adaptations of the deep-sea mussel Gigantidas platifrons and the shallow-water mussel Mytilus galloprovincialis to high hydrostatic pressure (HHP) conditions. By exposing atmospheric pressure (AP) acclimated G. platifrons and M. galloprovincialis to HHP, we aim to simulate extreme environmental challenges and assess their adaptive mechanisms. Through comparative transcriptomic analysis, we identified both conserved and species-specific mechanisms of adaptation, with a notable change in gene expression associated with immune system, substance transport, protein ubiquitination, apoptosis, lipid metabolism and antioxidant processes in both species. G. platifrons demonstrated an augmented lipid metabolism, whereas M. galloprovincialis exhibited a dampened immune function. Additionally, the expressed pattern of deep-sea mussel G. platifrons were more consistent than shallow-water mussel M. galloprovincialis under hydrostatic pressures changed conditions which corresponding the long-term living stable deep-sea environment. Moreover, evolutionary analysis pinpointed positively selected genes in G. platifrons that are linked to transmembrane transporters, DNA repair and replication, apoptosis, ubiquitination which are important to cell structural integrity, substances transport, and cellular growth regulation. This indicates a specialized adaptation strategy in G. platifrons to cope with the persistent HHP conditions of the deep sea. These results offer significant insights into the molecular underpinnings of mussel adaptation to varied hydrostatic conditions and enhance our comprehension of the evolutionary forces driving their depth-specific adaptations.
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Affiliation(s)
- Zhaoshan Zhong
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Guo
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Li Zhou
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China
| | - Hao Chen
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chao Lian
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Wang
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Huan Zhang
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lei Cao
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yan Sun
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Minxiao Wang
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Chaolun Li
- Center of Deep-sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 10049, China; Laoshan Laboratory, Qingdao 266237, China.
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Chen J, Zeng H, Lv W, Sun N, Wang C, Xu W, Hu M, Gan X, He L, He S, Fang C. Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2251-8. [PMID: 36648612 DOI: 10.1007/s11427-022-2251-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023]
Abstract
High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.
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Affiliation(s)
- Jie Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Xu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingliang Hu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lisheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chengchi Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Martín-Hernández R, Rodríguez-Canul R, Kantún-Moreno N, Olvera-Novoa MA, Medina-Contreras O, Garikoitz-Legarda C, Triviño JC, Zamora-Briseño JA, May-Solis V, Poot-Salazar A, Pérez-Vega JA, Gil-Zamorano J, Grant G, Dávalos A, Olivera-Castillo L. Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus. Int J Mol Sci 2021; 22:ijms22083882. [PMID: 33918680 PMCID: PMC8070510 DOI: 10.3390/ijms22083882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.
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Affiliation(s)
- Roberto Martín-Hernández
- Bioinformatics and Biostatistics Unit, IMDEA Food Institute, CEI UAM+CSIC, Carretera de Cantoblanco 8, 28049 Madrid, Spain;
| | - Rossanna Rodríguez-Canul
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Nuvia Kantún-Moreno
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Miguel A. Olvera-Novoa
- Laboratorio de Nutrición Acuícola, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (M.A.O.-N.); (V.M.-S.)
| | - Oscar Medina-Contreras
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México “Federico Gómez”, Mexico City 06720, Mexico;
| | - Cristobal Garikoitz-Legarda
- Bioinformatics Department, Sistemas Genómicos S.L., Ronda de Guglielmo Marconi 6, 46980 Paterna, Spain; (C.G.-L.); (J.C.T.)
| | - Juan Carlos Triviño
- Bioinformatics Department, Sistemas Genómicos S.L., Ronda de Guglielmo Marconi 6, 46980 Paterna, Spain; (C.G.-L.); (J.C.T.)
| | - Jesús Alejandro Zamora-Briseño
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Víctor May-Solis
- Laboratorio de Nutrición Acuícola, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (M.A.O.-N.); (V.M.-S.)
| | - Alicia Poot-Salazar
- Centro Regional de Investigaciones Acuícola y Pesqueras en Yucalpetén, Instituto Nacional de Pesca y Acuacultura, Boulevard del Pescador S/N, Puerto de Abrigo, Progreso 97320, Yucatán, Mexico;
| | - Juan Antonio Pérez-Vega
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Judit Gil-Zamorano
- Laboratory of Epigenetics of Lipid Metabolism, IMDEA Food Institute, CEI UAM+CSIC, Carretera de Cantoblanco 8, 28049 Madrid, Spain;
| | - George Grant
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Correspondence: (G.G.); (A.D.); (L.O.-C.)
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, IMDEA Food Institute, CEI UAM+CSIC, Carretera de Cantoblanco 8, 28049 Madrid, Spain;
- Correspondence: (G.G.); (A.D.); (L.O.-C.)
| | - Leticia Olivera-Castillo
- Laboratorio de Nutrición Acuícola, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (M.A.O.-N.); (V.M.-S.)
- Correspondence: (G.G.); (A.D.); (L.O.-C.)
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Li X, Wang C, Li N, Gao Y, Ju Z, Liao G, Xiong D. Combined Effects of Elevated Temperature and Crude Oil Pollution on Oxidative Stress and Apoptosis in Sea Cucumber ( Apostichopus japonicus, Selenka). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18020801. [PMID: 33477823 PMCID: PMC7832845 DOI: 10.3390/ijerph18020801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 01/15/2023]
Abstract
Currently, global climate change and oil pollution are two main environmental concerns for sea cucumber (Apostichopus japonicus) aquaculture. However, no study has been conducted on the combined effects of elevated temperature and oil pollution on sea cucumber. Therefore, in the present study, we treated sea cucumber with elevated temperature (26 °C) alone, water-accommodated fractions (WAF) of Oman crude oil at an optimal temperature of 16 °C, and Oman crude oil WAF at an elevated temperature of 26 °C for 24 h. Results showed that reactive oxygen species (ROS) level and total antioxidant capacity in WAF at 26 °C treatment were higher than that in WAF at 16 °C treatment, as evidenced by 6.03- and 1.31-fold-higher values, respectively. Oxidative damage assessments manifested that WAF at 26 °C treatment caused much severer oxidative damage of the biomacromolecules (including DNA, proteins, and lipids) than 26 °C or WAF at 16 °C treatments did. Moreover, compared to 26 °C or WAF at 16 °C treatments, WAF at 26 °C treatment induced a significant increase in cellular apoptosis by detecting the caspase-3 activity. Our results revealed that co-exposure to elevated temperature and crude oil could simulate higher ROS levels and subsequently cause much severer oxidative damage and cellular apoptosis than crude oil alone on sea cucumber.
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Affiliation(s)
- Xishan Li
- National Marine Environmental Monitoring Center, Dalian 116023, China; (X.L.); (N.L.); (Z.J.)
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; (C.W.); (D.X.)
- State Environmental Protection Key Laboratory of Coastal Ecosystem, Dalian 116023, China
| | - Chengyan Wang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; (C.W.); (D.X.)
| | - Nan Li
- National Marine Environmental Monitoring Center, Dalian 116023, China; (X.L.); (N.L.); (Z.J.)
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; (C.W.); (D.X.)
| | - Yali Gao
- School of Marine Engineering, Jimei University, Xiamen 361021, China;
| | - Zhonglei Ju
- National Marine Environmental Monitoring Center, Dalian 116023, China; (X.L.); (N.L.); (Z.J.)
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; (C.W.); (D.X.)
| | - Guoxiang Liao
- National Marine Environmental Monitoring Center, Dalian 116023, China; (X.L.); (N.L.); (Z.J.)
- State Environmental Protection Key Laboratory of Coastal Ecosystem, Dalian 116023, China
- Correspondence: ; Tel.: +86-0411-8478-3810
| | - Deqi Xiong
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; (C.W.); (D.X.)
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