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Perillo M, Sepe RM, Paganos P, Toscano A, Annunziata R. Sea cucumbers: an emerging system in evo-devo. EvoDevo 2024; 15:3. [PMID: 38368336 PMCID: PMC10874539 DOI: 10.1186/s13227-023-00220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/24/2023] [Indexed: 02/19/2024] Open
Abstract
A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.
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Affiliation(s)
- Margherita Perillo
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA, 02543, USA.
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Rosa Maria Sepe
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Periklis Paganos
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Alfonso Toscano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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Jiang J, Gao S, Zhao Z, Chen Z, Zhang F, Li L, Jiang P, Guan X, Li P, Pan Y, Zhou Z. A novel short-type peptidoglycan recognition protein with unique polysaccharide recognition specificity in sea cucumber, Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109263. [PMID: 38040134 DOI: 10.1016/j.fsi.2023.109263] [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: 09/21/2023] [Revised: 11/22/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Pattern recognition receptors (PRRs) are the first line of immune defense in invertebrates against pathogen infection; they recognize pathogens and transmit signals to downstream immune pathways. Among these, peptidoglycan recognition proteins (PGRPs) are an important family in invertebrates that generally comprise of complicated isoforms. A comprehensive understanding of PGRPs in evolutionarily and economically important marine invertebrates, such as the sea cucumber, Apostichopus japonicus, is crucial. Previous studies have identified two PGRPs in sea cucumber, AjPGRP-S and AjPGRP-S1, and another novel short-type PGRP, AjPGRP-S3, was additionally identified here. The full-length cDNA sequence of AjPGRP-S3 was obtained here by PCR-RACE, followed by which showed its gene expression analyses by in situ hybridization that showed it to be relatively highly expressed in coelomocytes and tube feet. Based on an analysis of the recombinant protein, rAjPGRP-S3, a board-spectrum pathogen recognition ability was noted that covered diverse Gram-negative and -positive bacteria, and fungi. Moreover, according to the results of yeast two-hybridization, it was suggested that rAJPGRP-S3 interacted with multiple immune-related factors, including proteins involved in the complement system, extracellular matrix, vesicle trafficking, and antioxidant system. These findings prove the important functions of AjPGRP-S3 in the transduction of pathogen signals to downstream immune effectors and help explore the functional differences in the AjPGRP isoforms.
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Affiliation(s)
- Jingwei Jiang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Shan Gao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Zelong Zhao
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Zhong Chen
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Feifei Zhang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Li Li
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Pingzhe Jiang
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Xiaoyan Guan
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Peipei Li
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Yongjia Pan
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China
| | - Zunchun Zhou
- Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Key Laboratory of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, PR China.
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Zhao Y, Song M, Yu Z, Pang L, Zhang L, Karakassis I, Dimitriou PD, Yuan X. Transcriptomic Responses of a Lightly Calcified Echinoderm to Experimental Seawater Acidification and Warming during Early Development. BIOLOGY 2023; 12:1520. [PMID: 38132346 PMCID: PMC10740944 DOI: 10.3390/biology12121520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Ocean acidification (OA) and ocean warming (OW) are potential obstacles to the survival and growth of marine organisms, particularly those that rely on calcification. This study investigated the single and joint effects of OA and OW on sea cucumber Apostichopus japonicus larvae raised under combinations of two temperatures (19 °C or 22 °C) and two pCO2 levels (400 or 1000 μatm) that reflect the current and end-of-21st-century projected ocean scenarios. The investigation focused on assessing larval development and identifying differences in gene expression patterns at four crucial embryo-larval stages (blastula, gastrula, auricularia, and doliolaria) of sea cucumbers, using RNA-seq. Results showed the detrimental effect of OA on the early development and body growth of A. japonicus larvae and a reduction in the expression of genes associated with biomineralization, skeletogenesis, and ion homeostasis. This effect was particularly pronounced during the doliolaria stage, indicating the presence of bottlenecks in larval development at this transition phase between the larval and megalopa stages in response to OA. OW accelerated the larval development across four stages of A. japonicus, especially at the blastula and doliolaria stages, but resulted in a widespread upregulation of genes related to heat shock proteins, antioxidant defense, and immune response. Significantly, the negative effects of elevated pCO2 on the developmental process of larvae appeared to be mitigated when accompanied by increased temperatures at the expense of reduced immune resilience and increased system fragility. These findings suggest that alterations in gene expression within the larvae of A. japonicus provide a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Ocean School, Yantai University, Yantai 264005, China
| | - Mingshan Song
- Ministry of Ecology and Environment, National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Zhenglin Yu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Lei Pang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ioannis Karakassis
- Marine Ecology Laboratory, Department of Biology, University of Crete, GR 70013 Heraklion, Greece
| | - Panagiotis D. Dimitriou
- Marine Ecology Laboratory, Department of Biology, University of Crete, GR 70013 Heraklion, Greece
| | - Xiutang Yuan
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Ministry of Ecology and Environment, National Marine Environmental Monitoring Center, Dalian 116023, China
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4
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Sun H, Chen Z, Jiang J, Dong Y, Wang B, Guan X, Zhao L, Gao S, Zunchun Z. Analyses of regulation between miRNA and DNA methyltransferase 1 related genes in sea cucumber Apostichopusjaponicus. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109169. [PMID: 37852510 DOI: 10.1016/j.fsi.2023.109169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Affiliation(s)
- Hongjuan Sun
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Zhong Chen
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Jingwei Jiang
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China.
| | - Ying Dong
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Bai Wang
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Xiaoyan Guan
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Liang Zhao
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Shan Gao
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Zhou Zunchun
- Key Lab of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Key Laboratory of Germplasm Improvement and Fine Seed Breeding for Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China.
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Yu Y, Ding P, Huang X, Wang X, Zhao Z, Wang H, Ding J, Chang Y, Zhao C. Bacillus licheniformis reduces mortality, improves symptoms, and controls residual pathogenicity in juvenile sea cucumbers Apostichopus japonicus infected with skin ulceration syndrome. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106179. [PMID: 37742388 DOI: 10.1016/j.marenvres.2023.106179] [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: 05/21/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Mass mortality caused by skin ulceration syndrome (SUS) is the bottle-neck for the sustainable aquaculture of the sea cucumber Apostichopus japonicus. In the present study, probiotic Bacillus licheniformis (0.25 × 109 CFU/g) was used as the treatment for A. japonicus infected with the SUS that caused by Vibrio harveyi. We found that B. licheniformis significantly reduced the number of infected sea cucumbers 5 days and 7 days after the treatment (group B), compared to those without B. licheniformis treatment (group C) (P < 0.001; P < 0.001). Further, the sea cucumbers fed B. licheniformis had significantly lower mortality at the end of the experiment (<10%) than that of those without the B. licheniformis treatment (>60%) (P < 0.001). These results suggest that the treatment of B. licheniformis is an effective method to reduce the mass mortality resulted from SUS in sea cucumber aquaculture. Further, 3-5 days of treatment significantly improved the adverse symptoms of SUS on the physiology and behavior of sea cucumbers, including the righting behavior, adhesion behavior, food consumption, fecal output and mobility. This indicates B. licheniformis treatment has the advantage in the recovery of sea cucumbers after SUS. Moreover, there was no significant difference observed in the physiology and behavior of sea cucumbers between the SUS infected sea cucumbers after the 7-day treatment of B. licheniformis and the healthy individuals. SUS infected sea cucumbers effectively returned to a stage of normalcy. Further, we found a significantly lower infected rate in sea cucumbers exposed to the culture water of group B (∼5%) than that of those in exposure to the culture water of group C (∼60%). This indicates that the treatment of B. licheniformis efficiently controls the residual pathogenicity of SUS in culture water. The present study demonstrated the effectiveness of B. licheniformis treatment as an environmentally friendly approach to reducing mortality, improving symptoms, and controlling residual pathogenicity in sea cucumber aquaculture.
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Affiliation(s)
- Yushi Yu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Peng Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xiyuan Huang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xiajing Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zihe Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Huiyan Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Chong Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
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Hao P, Han L, Quan Z, Jin X, Li Y, Wu Y, Zhang X, Wang W, Gao C, Wang L, Wang H, Zhang W, Chang Y, Ding J. Integrative mRNA-miRNA interaction analysis associated with the immune response of Strongylocentrotus intermedius to Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108577. [PMID: 36773712 DOI: 10.1016/j.fsi.2023.108577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China and has experienced mass mortality owing to outbreaks of bacterial diseases such as black mouth disease. This has caused serious economic losses to the sea urchin farming industry. To investigate the immune response mechanism of S. intermedius with different tube feet colors in response to Vibrio harveyi infection, we examined the different tube feet-colored S. intermedius under V. harveyi challenge and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. We obtained 1813 differentially expressed genes (DEGs), 28 DE miRNAs, and 303 DE miRNA-DEG pairs in different tube feet-colored S. intermedius under V. harveyi challenge. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the most significant DEGs were associated with the Notch signaling and phagosome pathways. The target genes of immune-related miRNAs (miR-71, miR-184, miR-193) and genes (CALM1, SPSB4, DMBT, CSRP1) in S. intermedius were predicted and validated. This study provides insight into the molecular mechanisms that regulate genes involved in the immune response of S. intermedius infected with V. harveyi.
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Affiliation(s)
- Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China; Ningbo University, Ningbo, Zhejiang, 315832, PR China
| | - Zijiao Quan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Heng Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China.
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Yan T, Ai C, Ou H, Song S, Yang S, Yang J. The Intestinal Microbiota Involves in the Deterioration of Live Sea Cucumber During Storage. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2023. [DOI: 10.1080/10498850.2023.2174393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Tingting Yan
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, PR China
| | - Chunqing Ai
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, PR China
| | - Haoyang Ou
- Pre- architecture Design, Iowa State University, Ames, IA, USA
| | - Shuang Song
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, PR China
| | - Sheng Yang
- Roy J. Carver Dept. of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Jingfeng Yang
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, PR China
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Jiang J, Zhao Z, Gao S, Chen Z, Pan Y, Guan X, Jiang P, Li P, Wang B, Sun H, Dong Y, Zhou Z. Functions of lysin motif (LysM)-containing protein in antibacterial responses of sea cucumbers, Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2022; 131:1275-1281. [PMID: 36400371 DOI: 10.1016/j.fsi.2022.11.016] [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: 08/28/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
The lysin motif (LysM)-containing protein is one of widespread pattern-recognition receptors in prokaryotes and eukaryotes. Numerous LysM-containing gene sequences are present in gene databases; however, few have been well characterized, especially in echinoderms. In this study, the full-length cDNA of a novel LysM-containing gene was obtained from the sea cucumber Apostichopus japonicus, named AjLysM-1, using polymerase chain reaction (PCR) combined with rapid amplification of cDNA ends. We prepared and expressed recombinant AjLysM-1 protein (rAjLysM-1) and determined its pathogen-recognition ability by enzyme-linked immunosorbent and immunofluorescence assays. We also analyzed the tissue expression pattern and response to immune challenges of AjLysM-1 using quantitative real-time reverse transcription-PCR and in situ hybridization. The AjLysM-1 protein was predicted to be an intracellular non-secreted LysM-containing protein, highly homologous to the same protein in other marine echinoderms. AjLysM-1 transcripts were highest expressed in coelomocytes and were strikingly induced by challenge with representative bacterial and fungal polysaccharides. rAjLysM-1 showed weak binding to mannan, Pseudoalteromonas nigrifaciens, and Shewanella baltica, implying that AjLysM-1 might provide inadequate defense against Gram-negative bacteria and fungi. Notably, rAjLysM-1 also interacted with tyrosine protein kinase and filamin-B, indicating that it could be involved in focal adhesion in A. japonicus. These findings improve our understanding of the functions of LysM-containing proteins in marine echinoderms.
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Affiliation(s)
- Jingwei Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Shan Gao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zhong Chen
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Yongjia Pan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Pingzhe Jiang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Peipei Li
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Bai Wang
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Hongjuan Sun
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Ying Dong
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, PR China.
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Duan X, Shao Y, Che Z, Zhao X, Guo M, Li C, Liang W. Genome-wide identification m 6A modified circRNAs revealed their key roles in skin ulceration syndrome disease development in Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2022; 127:748-757. [PMID: 35835384 DOI: 10.1016/j.fsi.2022.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Circular RNAs (circRNAs) are novel endogenous non-coding RNAs (ncRNAs) and can be acted as competing endogenous RNAs (ceRNAs) to regulate microRNA (miRNA) and downstream gene expression. Recently, m6A modification has been found in circRNA, and m6A circRNAs also play important roles in various biological processes and a variety of diseases. Our previous study had been demonstrated that circRNAs were differentially expressed in skin ulceration syndrome (SUS) diseased sea cucumber Apostichopus japonicus. However, whether the function of circRNAs are dependent on m6A levels are largely unknown. Here, we firstly investigated the genome-wide map of m6A circRNAs in sea cucumbers with different stages of Vibrio splendidus challenge, that's Control group, SUS-diseased group, and SUS-resistant group. MeRIP-seq revealed that m6A abundances were enriched in circRNAs in all three groups, especially for SUS-resistant group. Among them, more than 62% of modified circRNAs harbor only a single m6A peak and about 55% of m6A sites in circRNAs were derived from sense overlapping in each group. After V. splendidus infection, we found that most of m6A peaks in circRNAs were upregulated and less were downregulated in both SUS-diseased and SUS-resistant groups when compared with Control. Furthermore, GO analysis indicated that the host genes of circRNAs with dysregulated m6A peaks in SUS-diseased and SUS-resistant groups were both mainly enriched in the adhesion pathway. More importantly, we discovered that more than 50% m6A circRNAs showed a positive correlation between the circRNAs expression and m6A methylation levels both in SUS-diseased and SUS-resistant groups. Therefore, a core circRNA-miRNA-mRNA (ceRNA) network whether influenced by m6A modification was constructed based on conjoint analysis. Our results indicated that several selected m6A circRNAs bind with miRNAs were mainly targeting to ubiquitylation system and adhesion pathway. What's more, three candidate m6A circRNAs and three target genes were validated by MeRIP-qPCR and qPCR, whose m6A levels in circRNA and mRNA expressions were consistent with disease occurrence or disease resistance. All of our current findings suggested that m6A circRNAs could play important roles during pathogen infection and might be served as a new molecular biomarker in SUS disease diagnose of A. japonicus.
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Affiliation(s)
- Xuemei Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China.
| | - Zhongjie Che
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Xuelin Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Ming Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
| | - Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China.
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10
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Sea Cucumber Body Vesicular Syndrome Is Driven by the Pond Water Microbiome via an Altered Gut Microbiota. mSystems 2022; 7:e0135721. [PMID: 35418244 PMCID: PMC9239130 DOI: 10.1128/msystems.01357-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apostichopus japonicus (sea cucumber) is one of the most valuable aquaculture species in China; however, different diseases can limit its economic development. Recently, a novel disease, body vesicular syndrome (BVS), was observed in A. japonicus aquaculture. Diseased animals displayed no obvious phenotypic characteristics; however, after boiling at the postharvest stage, blisters, lysis, and body ruptures appeared. In this study, a multiomics strategy incorporating analysis of the gut microbiota, the pond microbiome, and A. japonicus genotype was established to investigate BVS. Detailed analyses of differentially expressed proteins (DEPs) and metabolites suggested that changes in cell adhesion structures, caused by disordered fatty acid β-oxidation mediated by vitamin B5 deficiency, could be a putative BVS mechanism. Furthermore, intestinal dysbacteriosis due to microbiome variations in pond water was considered a potential reason for vitamin B5 deficiency. Our BVS index, based on biomarkers identified from the A. japonicus gut microbiota, was a useful tool for BVS diagnosis. Finally, vitamin B5 supplementation was successfully used to treat BVS, suggesting an association with BVS etiology. IMPORTANCE Body vesicular syndrome (BVS) is a novel disease in sea cucumber aquaculture. As no phenotypic features are visible, BVS is difficult to confirm during aquaculture and postharvest activities, until animals are boiled. Therefore, BVS could lead to severe economic losses compared with other diseases in sea cucumber aquaculture. In this study, for the first time, we systematically investigated BVS pathogenesis and proposed an effective treatment for the condition. Moreover, based on the gut microbiota, we established a noninvasive diagnostic method for BVS in sea cucumber.
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Figueroa Á, Brante A, Cárdenas L. RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis. Sci Rep 2021; 11:14997. [PMID: 34294855 PMCID: PMC8298564 DOI: 10.1038/s41598-021-94646-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
The polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.
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Affiliation(s)
- Álvaro Figueroa
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.
| | - Antonio Brante
- Facultad de Ciencias, Centro de Investigación en Biodiversidad y Ambientes Sustentables, Universidad Católica de la Ssma, Concepción, Concepción, Chile
- Departamento Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Leyla Cárdenas
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Centro Fondap-IDEAL, Valdivia, Chile
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12
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Zhao Z. Comparison of microbial communities and the antibiotic resistome between prawn mono- and poly-culture systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111310. [PMID: 32937228 DOI: 10.1016/j.ecoenv.2020.111310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.
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Affiliation(s)
- Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, PR China.
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13
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Delroisse J, Van Wayneberghe K, Flammang P, Gillan D, Gerbaux P, Opina N, Todinanahary GGB, Eeckhaut I. Epidemiology of a SKin Ulceration Disease (SKUD) in the sea cucumber Holothuria scabra with a review on the SKUDs in Holothuroidea (Echinodermata). Sci Rep 2020; 10:22150. [PMID: 33335179 PMCID: PMC7746772 DOI: 10.1038/s41598-020-78876-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/18/2020] [Indexed: 01/04/2023] Open
Abstract
Aquacultivated sea cucumbers often suffer from SKin Ulceration Diseases (SKUDs). SKUDs have been observed in six holothuroid species from nine countries. All SKUDs present a similar symptom-the skin ulceration-and can be induced by bacteria, viruses, or abiotic factors. We here provide an update on SKUDs in holothuroids and analyse the case of the SKUD observed in Holothuria scabra in Madagascar. Field observations revealed a seasonality of the disease (i.e. wintertime maximum peak). Morphological analyses of integument ulcers showed that sea cucumbers react by forming a collagen fibre plug. Metagenomic analyses revealed a higher proportion of Vibrionaceae (Gammaproteobacteria) in ulcers in comparison to the healthy integument of the same individuals. Experimental infection assays were performed with ulcer crude extracts and bacteria isolated from these extracts (e.g. Vibrio parahaemolyticus) but did not significantly induce skin ulceration. Our results suggest that the disease is not induced by a pathogen or, at the very least, that the pathogen is not found within the ulcers as the disease is not transmissible by contact. An initial cause of the SKUD in Madagascar might be the repeated and prolonged exposures to cold temperatures. Opportunistic bacteria could settle in the dermis of ulcerated individuals and promote the ulcer extension. We propose a general nomenclature for SKUDs based on the acronym of the disease, the affected sea cucumber species (e.g. Hs for Holothuria scabra), the concerned region using an ISO code 3166-2 (e.g. MG for Madagascar), the description date (e.g. 20 for the year 2020), and, when known, the inducing agent (first letter of the general taxon, b for bacteria, v for virus in currently known cases; a a if it is an abiotic inducing parameter; nothing if the inducing cause has not been precisely identified). The disease described in this work will be designated under the name SKUD Hs-MG-20.
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Affiliation(s)
- Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons - UMONS, Place du Parc, 6, 7000, Mons, Belgium. .,Marine Station of Belaza, Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Route du Port Mahavatse II, P.O. Box 141, 601, Toliara, Madagascar.
| | - Kévin Van Wayneberghe
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons - UMONS, Place du Parc, 6, 7000, Mons, Belgium
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons - UMONS, Place du Parc, 6, 7000, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons - UMONS, Place du Parc, 6, 7000, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Lab, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons - UMONS, Place du Parc, 6, 7000, Mons, Belgium
| | - Noel Opina
- Madagascar Holothurie (R&D of Indian Ocean Trepang), Toliara, Route du Port Mahavatse II, P.O. Box 141, 601, Toliara, Madagascar
| | - Gildas Georges Boleslas Todinanahary
- Marine Station of Belaza, Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Route du Port Mahavatse II, P.O. Box 141, 601, Toliara, Madagascar.,Madagascar Holothurie (R&D of Indian Ocean Trepang), Toliara, Route du Port Mahavatse II, P.O. Box 141, 601, Toliara, Madagascar
| | - Igor Eeckhaut
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons - UMONS, Place du Parc, 6, 7000, Mons, Belgium. .,Marine Station of Belaza, Institut Halieutique et des Sciences Marines (IH.SM), University of Toliara, Route du Port Mahavatse II, P.O. Box 141, 601, Toliara, Madagascar. .,Madagascar Holothurie (R&D of Indian Ocean Trepang), Toliara, Route du Port Mahavatse II, P.O. Box 141, 601, Toliara, Madagascar.
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14
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Sun H, Zhou Z, Dong Y, Yang A, Jiang J. Insights into the DNA methylation of sea cucumber Apostichopus japonicus in response to skin ulceration syndrome infection. FISH & SHELLFISH IMMUNOLOGY 2020; 104:155-164. [PMID: 32502611 DOI: 10.1016/j.fsi.2020.05.005] [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: 11/23/2019] [Revised: 03/23/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an important epigenetic modification that regulates gene expression in many biological processes, including immune response. In this study, whole-genome bisulfite sequencing (WGBS) was carried out on healthy body wall (HB) and skin ulceration syndrome (SUS) infected body wall (SFB) to gain insights into the epigenetic regulatory mechanism in sea cucumber Apostichopus japonicus. After comparison, a total of 116,522 differentially methylated regions (DMRs) were obtained including 67,269 hyper-methylated and 49,253 hypo-methylated DMRs (p < 0.05, FDR < 0.001). GO enrichment analysis indicated that regulation of DNA-templated transcription (GO: 0006355), where DNA methylation occurred, was the most significant term in the biology process. The integration of methylome and transcriptome analysis revealed that 10,499 DMRs were negatively correlated with 496 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were enriched in the phosphoinositide 3-kinase-protein kinase B (PI3K/Akt)/mammalian target of rapamycin (mTOR) signaling pathway. Interestingly, two serine/threonine-protein kinases, nemo-like kinase (NLK) and mTOR, were highlighted after functional analysis. The variations of methylation in these two genes were associated with SUS infection and immune regulation. They regulated gene expression at different levels and showed interaction during response process. The validation of methylation sites showed high consistency between pyrosequencing and WGBS. WGBS analysis not only revealed the changes of DNA methylation, but also presented important information about the regulation of key genes after SUS infection in A. japonicus.
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Affiliation(s)
- Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
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15
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Zhong R, Liu S, Wang X, Zhang G, Gong N, Wang M, Sun Y. A real-time isothermal amplification based portable microfluidic system for simple and reliable detection of Vibrio splendidus. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2985-2994. [PMID: 32930158 DOI: 10.1039/d0ay00566e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The spread of infectious diseases among aquaculture species has a serious impact on the aquaculture industry. Simple, specific and low-cost detection methods are urgently needed for early diagnosis and timely treatment, particularly for on-site identifying and tracking of pathogens. Vibrio splendidus (V. splendidus) is regarded as one of the main pathogenic bacteria causing skin ulcerative syndrome in cultured sea cucumbers, leading to massive mortality and severe economic losses. We herein present a microfluidic-based real-time fluorogenic loop-mediated isothermal amplification (LAMP) system for simple and reliable detection of V. splendidus. A LAMP primer set with six primers (arsB1) specifically targeting the arsB gene of V. splendidus was successfully designed and tested on the portable microfluidic system for the first time. Only a single step of sample loading using a pipette is required to fill an array of reaction wells (with 10 or 18 wells) in a disposable chip for multiplex detection. A dedicated plastic shell is then utilized to tightly seal the openings of the chip by buckling to prevent contamination and evaporation. Up to four chips (one sample per chip) can be held in the stand-alone and inexpensive microdevice simultaneously, enabling on-demand detection of multiple samples in a single run. Reproducible (relatively low intra- and inter-chip variability) and sensitive (as few as ∼20 CFU, Colony-Forming Units, per reaction well) on-chip arsB1-LAMP assay was demonstrated by using diluted lysate of V. splendidus. A linear standard curve (R2 > 0.98) was attained over the template concentration range of 5 × 103 to 5 × 106 CFU mL-1. V. splendidus can be detected in samples containing different bacteria, indicating the feasibility of the portable microfluidic LAMP system for parallel detection of multiple bacterial pathogens. The proposed on-chip LAMP assay is simple to operate, reliable for amplification, flexible in detection and cost-effective in instrumentation and testing, holding great potential for on-site rapid detection and routine monitoring of aquaculture pathogens.
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Affiliation(s)
- Runtao Zhong
- Institute of Environmental Systems Biology, Dalian Maritime University, 1 Linghai Road, Dalian 116026, China.
| | - Shilin Liu
- Institute of Environmental Systems Biology, Dalian Maritime University, 1 Linghai Road, Dalian 116026, China.
| | - Xiaohui Wang
- Dalian University, Dalian Economic & Technical Development Zone, Dalian 116622, China
| | - Guohao Zhang
- Beijing Baicare Biotechnology Co., Ltd., Zhongguancun Life Science Park, Beijing 102206, China
| | - Ning Gong
- Institute of Environmental Systems Biology, Dalian Maritime University, 1 Linghai Road, Dalian 116026, China.
| | - Mengyu Wang
- Institute of Environmental Systems Biology, Dalian Maritime University, 1 Linghai Road, Dalian 116026, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, Dalian Maritime University, 1 Linghai Road, Dalian 116026, China.
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16
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Liang L, Chen J, Li Y, Zhang H. Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures. BMC Genomics 2020; 21:68. [PMID: 31964339 PMCID: PMC6974979 DOI: 10.1186/s12864-020-6480-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Background Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood. Results In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa. Conclusions Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.
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Affiliation(s)
- Linying Liang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiawei Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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17
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Guerra V, Haynes G, Byrne M, Yasuda N, Adachi S, Nakamura M, Nakachi S, Hart MW. Nonspecific expression of fertilization genes in the crown-of-thorns Acanthaster cf. solaris: Unexpected evidence of hermaphroditism in a coral reef predator. Mol Ecol 2019; 29:363-379. [PMID: 31837059 DOI: 10.1111/mec.15332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 01/04/2023]
Abstract
The characterization of gene expression in gametes has advanced our understanding of the molecular basis for ecological variation in reproductive success and the evolution of reproductive isolation. These advances are especially significant for ecologically important keystone predators such as the coral-eating crown-of-thorns sea stars (COTS, Acanthaster) which are the most influential predator species in Indo-Pacific coral reef ecosystems and the focus of intensive management efforts. We used RNA-seq and transcriptome assemblies to characterize the expression of genes in mature COTS gonads. We described the sequence and domain organization of eight genes with sex-specific expression and well known functions in fertilization in other echinoderms. We found unexpected expression of genes in one ovary transcriptome that are characteristic of males and sperm, including genes that encode the sperm-specific guanylate cyclase receptor for an egg pheromone, and the sperm acrosomal protein bindin. In a reassembly of previously published RNA-seq data from COTS testes, we found a complementary pattern: strong expression of four genes that are otherwise well known to encode egg-specific fertilization proteins, including the egg receptor for bindin (EBR1) and the acrosome reaction-inducing substance in the egg coat (ARIS1, ARIS2, ARIS3). We also found histological evidence of both eggs and sperm developing in the same gonad in several COTS individuals from a parallel study. These results suggest the occurrence of hermaphrodites, and the potential for reproductive assurance via self-fertilization. Our findings have implications for management of COTS populations, especially in consideration of the large size and massive fecundity of these sea stars.
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Affiliation(s)
- Vanessa Guerra
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Gwilym Haynes
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.,Department of Biology, Langara College, Vancouver, British Columbia, Canada
| | - Maria Byrne
- Schools of Medical and Biological Sciences, The University of Sydney, Sydney, Australia
| | - Nina Yasuda
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Souta Adachi
- School of Marine Science and Technology, Tokai University, Shimizu, Shizuoka, Japan
| | - Masako Nakamura
- School of Marine Science and Technology, Tokai University, Shimizu, Shizuoka, Japan
| | | | - Michael W Hart
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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18
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Zhang W, Wang Z, Leng X, Jiang H, Liu L, Li C, Chang Y. Transcriptome sequencing reveals phagocytosis as the main immune response in the pathogen-challenged sea urchin Strongylocentrotus intermedius. FISH & SHELLFISH IMMUNOLOGY 2019; 94:780-791. [PMID: 31585247 DOI: 10.1016/j.fsi.2019.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/25/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
The clarification of host immune responses to causative bacteria of spotting disease in the sea urchin Strongylocentrotus intermedius is vital to preventing and controlling this disease, especially to selective breeding for disease resistance. For this purpose, sea urchins were challenged with the causative bacterium Vibrio sp. to obtain spotting diseased and undiseased samples. We conducted next-generation sequencing to assess the key genes/pathways in control (CG), diseased (DG), and undiseased (UG) groups. A total of 454.1 million clean reads were obtained and assembled into 23,899 UniGenes with an N50 of 1359 bp, with 86.11% of them matching the genome sequence of the sea urchin S. purpuratus. A total of 8415 UniGenes were mapped to the non-redundant database. Salmon expression analysis revealed 725 significantly differentially expressed genes (DEGs) among CG, DG, and UG. These DEGs were enriched into 72 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including a core set of immune correlated pathways notably in the phagosome, vitamin digestion and absorption, Wnt signaling, and Notch signaling pathways. DG was evidently upregulated in these immune pathways and could enhance phagocytosis directly or indirectly. Thus, phagocytosis was the main coelomic cellular immune response in S. intermedius challenged by spotting disease causative bacterium. The expression patterns of 10 DEGs were confirmed via RT-qPCR, and the expression levels were consistent with the results of RNA-seq. Furthermore, 9899 SSRs were identified, and 123,692, 151,827, and 114,368 candidate SNPs were identified from CG, DG, and UG, respectively. These results provide basic information for our understanding of sea urchin antibacterial immunity.
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Affiliation(s)
- Weijie Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Zhong Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Xiaofei Leng
- Dalian Haibao Fishery, CO., Ltd, Dalian, 116041, PR China
| | - Huijie Jiang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China
| | - Lei Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China
| | - Chenghua Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang Province, 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, PR China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, PR China.
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19
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Zhao X, Duan X, Fu J, Shao Y, Zhang W, Guo M, Li C. Genome-Wide Identification of Circular RNAs Revealed the Dominant Intergenic Region Circularization Model in Apostichopus japonicus. Front Genet 2019; 10:603. [PMID: 31312211 PMCID: PMC6614181 DOI: 10.3389/fgene.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) were recently recognized to act as competing endogenous RNAs and play roles in gene expression regulation. Previous studies in humans and silkworms have shown that circRNAs take part in immune regulation. Here, we conducted coelomocyte circRNA sequencing to explore its immune functions in healthy and skin ulceration syndrome (SUS)-diseased sea cucumbers. A total of 3,592 circRNAs were identified in libraries with diversified circularization patterns compared with animal models. The common intron-pairing-driven circularization models are not popular in sea cucumber genome, which was replaced with intergenic region circularization. The accuracy of these identified circRNAs was further validated by Sanger sequencing and RNase R-treated assays. Expression profile analysis indicated that 117 circRNAs were upregulated and 144 circRNAs were downregulated in SUS-diseased condition, of which 71.6% were intergenic-type circRNAs. The interaction network of differentially expressed circRNAs and microRNAs (miRNAs) was constructed and showed that miR-2008 and miR-31, detected with significantly differential expression in SUS-affected samples in a previous study, were predicted to be regulated by 10 and 11 differentially expressed circRNAs with more than 10 binding sites, respectively. Moreover, seven circRNAs were further validated by quantitative real-time PCR, whose variation trends were consistent with circRNA sequencing. All our results supported that intergenic-type circRNAs might have a dominant function in Apostichopus japonicas immune response by acting as miRNA regulators.
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Affiliation(s)
- Xuelin Zhao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Xuemei Duan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Jianping Fu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Yina Shao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Weiwei Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Ming Guo
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
| | - Chenghua Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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20
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Lv Z, Guo M, Li C, Shao Y, Zhao X, Zhang W. Divergent proteomics response of Apostichopus japonicus suffering from skin ulceration syndrome and pathogen infection. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:196-205. [PMID: 30897459 DOI: 10.1016/j.cbd.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
Skin ulceration syndrome (SUS) of sea cucumber is a common and serious disease that affects the stable development of Apostichopus japonicus in the culture industry. The part of sea cucumber that suffers from major injury and is directly observed is the body wall, in which protein variations should be the most direct evidence of the disease. To understand the response mechanisms of A. japonicus in SUS progression, we investigated protein changes in the body wall of diseased A. japonicus induced by Vibrio splendidus and individuals with natural diseases by isobaric tags for relative and absolute quantification (iTRAQ). About 119 proteins were identified in the two iTRAQ groups. A comparison of the protein expression profiles among two SUS conditions revealed that the mode of action induced by V. splendidus (Vs-SUS) was completely different from those in individuals with natural disease (ND-SUS). Most of the differentially expressed proteins (DEPs) (33 in 37 DEPs) were significantly depressed in the Vs-SUS group. Only 13 proteins in 27 DEPs showed similar trend to those in the ND-SUS group. Many important proteins involved in major intercellular signaling pathways associated with SUS disease were identified based on the KEGG and GO database search. Many proteins were located in the mitochondria and mainly involved in the oxidative stress pathway. Glutathione metabolism pathway was associated with reactive oxygen (ROS) production in the ND-SUS group. In the Vs-group, most of the proteins were concentrated in the cytoplasm and were related to immunity and extracellular matrix stability. In the ND-SUS group, the activity of key enzymes (CAT, GPx) that eliminate mitochondrial ROS production and structural stable protein (HSP60, HSP10) decreased, whereas those of complement proteins (C3, C3-2) that promoted ROS production was upregulated. This finding supported that oxidative damage caused by ROS might be the main effector for SUS in the ND-SUS group. The challenge with V. splendidus led to the breakdown of the defense capability of sea cucumber and suppressed the expression of immune-related proteins, such as C-type lectin, caspase, STAT, and cystatin. The downregulation of TIMP led to MMP1 overexpression. Members of the MMP family could directly degrade the extracellular matrix, which may be the main reason for the cell matrix degradation and induced SUS disease in the Vs-SUS group. Hence, ROS and extracellular matrix degradation enzymes could play important roles in the formation of SUS in sea cucumber. Results provide insights into the complex molecular mechanism of SUS in sea cucumber.
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Affiliation(s)
- Zhimeng Lv
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Ming Guo
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yina Shao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Xuelin Zhao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
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21
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RNA Sequencing Analysis to Capture the Transcriptome Landscape during Tenderization in Sea Cucumber Apostichopus japonicus. Molecules 2019; 24:molecules24050998. [PMID: 30871127 PMCID: PMC6429463 DOI: 10.3390/molecules24050998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 12/27/2022] Open
Abstract
Sea cucumber (Apostichopus japonicus) is an economically significant species in China having great commercial value. It is challenging to maintain the textural properties during thermal processing due to the distinctive physiochemical structure of the A. japonicus body wall (AJBW). In this study, the gene expression profiles associated with tenderization in AJBW were determined at 0 h (CON), 1 h (T_1h), and 3 h (T_3h) after treatment at 37 °C using Illumina HiSeq™ 4000 platform. Seven-hundred-and-twenty-one and 806 differentially expressed genes (DEGs) were identified in comparisons of T_1h vs. CON and T_3h vs. CON, respectively. Among these DEGs, we found that two endogenous proteases-72 kDa type IV collagenase and matrix metalloproteinase 16 precursor-were significantly upregulated that could directly affect the tenderness of AJBW. In addition, 92 genes controlled four types of physiological and biochemical processes such as oxidative stress response (3), immune system process (55), apoptosis (4), and reorganization of the cytoskeleton and extracellular matrix (30). Further, the RT-qPCR results confirmed the accuracy of RNA-sequencing analysis. Our results showed the dynamic changes in global gene expression during tenderization and provided a series of candidate genes that contributed to tenderization in AJBW. This can help further studies on the genetics/molecular mechanisms associated with tenderization.
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Sun H, Zhou Z, Dong Y, Yang A, Pan Y, Jiang J, Chen Z, Guan X, Wang B, Gao S, Jiang B. In-depth profiling of miRNA regulation in the body wall of sea cucumber Apostichopus japonicus during skin ulceration syndrome progression. FISH & SHELLFISH IMMUNOLOGY 2018; 79:202-208. [PMID: 29763733 DOI: 10.1016/j.fsi.2018.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that mediate mRNA degradation or translation repression. Previous study showed that the expression of miRNAs was significantly changed in the body wall of sea cucumber Apostichopus japonicus after skin ulceration syndrome (SUS) infection, which is a dynamic process. However, the critical miRNAs from body wall that involved in different infection stages of SUS remain unknown. In this study, four cDNA libraries were constructed with the body wall from healthy and three SUS-infected stages of A. japonicus. A total of 248 conserved miRNAs and five novel miRNAs were identified through Illumina HiSeq 2000 platform. Compared to the control, 238 miRNAs showed significant differential expression at three stages of SUS progression. Totally, 3149 miRNA-mRNA pairs were identified by target prediction and 314 miRNA-mRNA pairs showed negative correlation. It is noteworthy that 15 miRNAs and four mRNAs were located at the crucial positions of the network built with the anti-correlated miRNA-mRNA pairs. GO and KEGG enrichment analysis indicated that the predicted targets were involved in many immune-related processes. Deep analysis of miR-31c-5p, miR-29b-3p, NF-kB, mucin 2 and titin showed that they may play important roles in the pathogens attachment and recognition, signaling transduction and lesions repair of A. japonicus after SUS infection. These results would be useful for further investigating the potential roles of critical miRNAs and mRNAs in A. japonicus immune regulation.
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Affiliation(s)
- Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China.
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Yongjia Pan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Zhong Chen
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Xiaoyan Guan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bai Wang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, PR China
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23
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Wang Z, Cui J, Song J, Wang H, Gao K, Qiu X, Gou M, Li X, Hu Z, Wang X, Chang Y. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:193-205. [PMID: 29492749 DOI: 10.1007/s10126-018-9796-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.
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Affiliation(s)
- Zhicheng Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jun Cui
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
| | - Haoze Wang
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Kailun Gao
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Meng Gou
- School of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Xin Li
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Ziwen Hu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
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24
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Proteomic analysis reveals the important roles of alpha-5-collagen and ATP5β during skin ulceration syndrome progression of sea cucumber Apostichopus japonicus. J Proteomics 2018; 175:136-143. [DOI: 10.1016/j.jprot.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/23/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
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