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Kim S, Lee S, Kim GJ, Sohn YC. Gene Expression Profiles of Long-Chain Acyl-Coenzyme A Dehydrogenase, Nuclear Distribution C-Containing Protein 3, and Receptor Tyrosine Kinase Tie-1 in Swimming Larva of Sea Cucumber Apostichopus japonicus. Dev Reprod 2023; 27:91-99. [PMID: 37529014 PMCID: PMC10390100 DOI: 10.12717/dr.2023.27.2.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/13/2023] [Accepted: 06/09/2023] [Indexed: 08/03/2023]
Abstract
The sea cucumber, Apostichopus japonicus, is one of the most valuable aquatic species. The color of body wall and appearance are important for the value of sea cucumbers. To examine expression pattern of long-chain acyl-coenzyme A dehydrogenase (LCAD), nuclear distribution C-containing protein 3 (NUDCD3), and receptor tyrosine kinase Tie-1 (TIE1), previously reported as differently expressed genes during the pigmentation of sea cucumber, we analyzed the temporal profiles of LCAD, NUDCD3, and TIE1 mRNAs in LED-exposed and light-shielded A. japonicus. Real-time quantitative PCR revealed that the LCAD, NUDCD3, and TIE1 mRNAs from the juveniles at 40-60 days post-fertilization (dpf) exhibited increasing patterns as compared to those of an early developmental larva (6-dpf). At 60-dpf juveniles, the LCAD and TIE1 mRNA levels of LED-exposed individuals were higher than those of light-shielded ones, whereas at 40-dpf and 50-dpf juveniles, the NUDCD3 mRNA expression was higher in the light-shielded condition (p<0.05). In the pigmented juveniles (90-dpf), the LCAD and TIE1 mRNA levels tended to show higher levels in red individuals than those in green ones, but there was a conversely higher level of NUDCD3 mRNA in green larva. In situ examination of LCAD and NUDCD3 mRNAs in light-shielded 6-dpf larva revealed that both genes are mainly expressed in the internal organs compared to the body surface. Together, these results may provide insights into the differential gene expression of LCAD, NUDCD3, and TIE1 during pigmentation process of the sea cucumber.
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Affiliation(s)
- Sehwan Kim
- Department of Marine Bioscience,
Gangneung-Wonju National University, Gangneung
25457, Korea
- Samcheok Fisheries Resource
Center, Samcheok 25932, Korea
| | - Seungheon Lee
- Department of Marine Bioscience,
Gangneung-Wonju National University, Gangneung
25457, Korea
| | - Gil Jung Kim
- Department of Marine Bioscience,
Gangneung-Wonju National University, Gangneung
25457, Korea
| | - Young Chang Sohn
- Department of Marine Bioscience,
Gangneung-Wonju National University, Gangneung
25457, Korea
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Wu S, Huang J, Li Y, Zhao L, Liu Z. Analysis of yellow mutant rainbow trout transcriptomes at different developmental stages reveals dynamic regulation of skin pigmentation genes. Sci Rep 2022; 12:256. [PMID: 34997156 PMCID: PMC8742018 DOI: 10.1038/s41598-021-04255-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022] Open
Abstract
Yellow mutant rainbow trout (YR), an economically important aquaculture species, is popular among consumers due to its excellent meat quality and attractive appearance. Skin color is a key economic trait for YR, but little is known about the molecular mechanism of skin color development. In this study, YR skin transcriptomes were analyzed to explore temporal expression patterns of pigmentation-related genes in three different stages of skin color development. In total, 16,590, 16,682, and 5619 genes were differentially expressed between fish at 1 day post-hatching (YR1d) and YR45d, YR1d and YR90d, and YR45d and YR90d. Numerous differentially expressed genes (DEGs) associated with pigmentation were identified, and almost all of them involved in pteridine and carotenoid synthesis were significantly upregulated in YR45d and YR90d compared to YR1d, including GCH1, PTS, QDPR, CSFIR1, SLC2A11, SCARB1, DGAT2, PNPLA2, APOD, and BCO2. Interestingly, many DEGs enriched in melanin synthesis pathways were also significantly upregulated, including melanogenesis (MITF, MC1R, SLC45A2, OCA2, and GPR143), tyrosine metabolism (TYR, TYRP1, and DCT), and MAPK signaling (KITA) pathways. Using short time-series expression miner, we identified eight differential gene expression pattern profiles, and DEGs in profile 7 were associated with skin pigmentation. Protein–protein interaction network analysis showed that two modules were related to xanthophores and melanophores. In addition, 1,812,329 simple sequence repeats and 2,011,334 single-nucleotide polymorphisms were discovered. The results enhance our understanding of the molecular mechanism underlying skin pigmentation in YR, and could accelerate the molecular breeding of fish species with valuable skin color traits and will likely be highly informative for developing new therapeutic approaches to treat pigmentation disorders and melanoma.
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Affiliation(s)
- Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Yongjuan Li
- College of Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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Integrative mRNA-miRNA interaction analysis reveals the molecular mechanism of skin color variation between wild-type and yellow mutant rainbow trout (Oncorhynchus mykiss). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100914. [PMID: 34653947 DOI: 10.1016/j.cbd.2021.100914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022]
Abstract
Rainbow trout (Oncorhynchus mykiss) is an important economic fish in China. Skin color affects the economic value of trout. However, the molecular mechanism of the skin color variation between wild-type (WR) and yellow mutant rainbow trout (YR) is unclear. We sequenced mRNAs and miRNAs of dorsal skin to identify key color variation-associated mRNAs and miRNAs between WR and YR. Overall, 2060 out of 3625 differentially expressed genes were upregulated in YR, and 196 out of 275 differentially expressed miRNAs were downregulated in WR. We identified three key YR-upregulated genes related to the formation of xanthophores (GCH1, SLC2A11, and SOX10). Interestingly, several genes related to melanogenesis (TYR, TYRP1, TYRP2, MC1R, MITF, PMEL, SLC45A2, and OCA2) were downregulated in WR. Integrated analysis identified five miRNAs that target at least two skin color-related genes (miR-495-y, miR-543-y, miR-665-z, miR-433-y, and miR-382-x). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of target genes identified noncoding RNA metabolic process as the most significantly enriched GO term, and several metabolic pathways associated with skin color were enriched significantly, such as tyrosine metabolism, histidine metabolism, and vitamin B6 metabolism. Quantitative real-time PCR of selected mRNAs and miRNAs validated the reliability of the integrated analysis. This study provides in-depth insights into the molecular mechanism of skin color variation between WR and YR, which will accelerate the genetic selection and breeding of rainbow trout with consumer-favored traits.
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Metabolomic analysis of white, green and purple morphs of sea cucumber Apostichopus japonicus during body color pigmentation process. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100827. [PMID: 33894529 DOI: 10.1016/j.cbd.2021.100827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/03/2021] [Accepted: 03/21/2021] [Indexed: 11/23/2022]
Abstract
The sea cucumber Apostichopus japonicus is an important economic species owing to their high nutritive and medicinal value. Body color is one of the most important traits in the cultivation, which affects taste and market price of holothurian products. Pigmentation is an important stage of sea cucumber growth and development, in addition to achieving rare and beautiful coloration. In this study, UHPLC-QTOF/MS technique was performed to analyze the metabolome of white, green and purple A. japonicus body wall during the pigmentation process. A total of 2633 metabolites were identified. OPLS-DA clearly discriminated the body wall metabolites among the three color morphs. In addition, 13 annotated metabolites that could discriminate white, green and purple A. japonicus were screened out. KEGG metabolic pathway analysis revealed that "biosynthesis of unsaturated fatty acids" and "fatty acid biosynthesis" were closely related in the different color morphs. Furthermore, we performed comparative analysis of polysaccharide and saponin among white, green and purple A. japonicus. The results showed that the content of polysaccharide and saponin in purple A. japonicus was the highest, while that in white A. japonicus was the lowest. This study will provide valuable information for future studies on sea cucumber and the molecular mechanism underlying pigmentation and color polymorphism, and may contribute to support the culturing of desirable color morphs.
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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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Auffret P, Le Luyer J, Sham Koua M, Quillien V, Ky CL. Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing. BMC Genomics 2020; 21:662. [PMID: 32977773 PMCID: PMC7517651 DOI: 10.1186/s12864-020-07015-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the black-lipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression. The relationship of shell colour with resulting cultured pearl colour is of great economic interest in P. margaritifera, on which a pearl industry is based. Hence, the albino phenotype provides a useful way to examine the molecular mechanisms underlying pigmentation. RESULTS Whole transcriptome RNA-sequencing analysis comparing albino and black wild-type phenotypes at three stages over the culture cycle of P. margaritifera revealed a total of 1606, 798 and 187 differentially expressed genes in whole juvenile, adult mantle and pearl sac tissue, respectively. These genes were found to be involved in five main molecular pathways, tightly linked to known pigmentation pathways: melanogenesis, calcium signalling pathway, Notch signalling pathway, pigment transport and biomineralization. Additionally, significant phenotype-associated SNPs were selected (N = 159), including two located in the Pif biomineralization gene, which codes for nacre formation. Interestingly, significantly different transcript splicing was detected between juvenile (N = 1366) and adult mantle tissue (N = 313) in, e.g., the tyrosinase Tyr-1 gene, which showed more complex regulation in mantle, and the Notch1 encoding gene, which was upregulated in albino juveniles. CONCLUSION This multiple RNA-seq approach provided new knowledge about genes associated with the P. margaritifera albino phenotype, highlighting: 1) new molecular pathways, such as the Notch signalling pathway in pigmentation, 2) associated SNP markers with biomineraliszation gene of interest like Pif for marker-assisted selection and prevention of inbreeding, and 3) alternative gene splicing for melanin biosynthesis implicating tyrosinase.
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Affiliation(s)
- Pauline Auffret
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
| | - Jérémy Le Luyer
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
| | - Manaarii Sham Koua
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
| | - Virgile Quillien
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
- Ifremer, UMR LEMAR UBO CNRS Ifremer IRD 6539, ZI Pointe Diable CS 10070, F-29280 Plouzane, France
| | - Chin-Long Ky
- Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française France
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34090 Montpellier, France
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Wu X, Chen T, Huo D, Yu Z, Ruan Y, Cheng C, Jiang X, Ren C. Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge. BMC Genomics 2020; 21:306. [PMID: 32299355 PMCID: PMC7161275 DOI: 10.1186/s12864-020-6698-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 03/24/2020] [Indexed: 12/18/2022] Open
Abstract
Background The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq. Results Sea cucumber primary coelomocytes were isolated from healthy H. leucospilota and incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactived Vibrio harveyi (107 cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R2 = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twenty-one cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h. Conclusion A de novo transcriptome was sequenced and assembled to generate the gene expression profiling across the sea cucumber coelomocytes treated with LPS, Poly (I:C) and V. harveyi. The cytokine genes identified in DEGs could be classified into 4 cytokine families, in which the expression of IL-17 family cytokines was most significantly induced after 10 μg/ml LPS challenge for 24 h. Our findings have laid the foundation not only for the research of molecular mechanisms related to the immune response in echinoderms but also for their origins in chordates, particularly in higher vertebrates.
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Affiliation(s)
- Xiaofen Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China
| | - Da Huo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China
| | - Zonghe Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China
| | - Yao Ruan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chuhang Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China. .,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, Guangzhou, PR China. .,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, People's Republic of China.
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Rise ML, Martyniuk CJ, Chen M. Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100603. [PMID: 31260856 DOI: 10.1016/j.cbd.2019.100603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Omics-technologies have revolutionized biomedical research over the past two decades, and are now poised to play a transformative role in aquaculture. This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (CBPD), with the objective to showcase the state-of-the-science for Omics in aquaculture. In this editorial, we describe the role that Omics can play in aquaculture, and provide a synopsis for each of the Special Issue articles that use these technologies to improve aquaculture practices. Current genomic resources available for some aquaculture species are also described. The number of datasets is impressive for species such as Atlantic salmon and rainbow trout, totaling in the thousands (NCBI Gene Expression Omnibus and Sequence Read Archive). We present a conceptual framework that describes how Omics can be leveraged to understand complex responses of aquatic animals in culture for relevant physiological outcomes, such as fecundity, growth, and immunity. Lastly, knowledge gaps and new directions are identified to address current obstacles in aquaculture. Articles in this Special Issue on aquaculture in CBPD highlight the diversity and scope of Omics in aquaculture. As the technology becomes more cost-effective, it is anticipated that genomics, transcriptomics, proteomics, metabolomics and lipidomics will play increasingly important roles in stock diagnostics (e.g. genetics, health, performance). The timing is right, as global concerns are reaching critical levels over food availability/security and water restrictions for humankind.
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Affiliation(s)
- Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.
| | - Muyan Chen
- College of Fisheries, Ocean University of China, Qingdao 266003, China
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Zhan Y, Lin K, Ge C, Che J, Li Y, Cui D, Pei Q, Liu L, Song J, Zhang W, Chang Y. Comparative transcriptome analysis identifies genes associated with papilla development in the sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:255-263. [DOI: 10.1016/j.cbd.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
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