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Campli G, Volovych O, Kim K, Veldsman WP, Drage HB, Sheizaf I, Lynch S, Chipman AD, Daley AC, Robinson-Rechavi M, Waterhouse RM. The moulting arthropod: a complete genetic toolkit review. Biol Rev Camb Philos Soc 2024. [PMID: 39039636 DOI: 10.1111/brv.13123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Exoskeletons are a defining character of all arthropods that provide physical support for their segmented bodies and appendages as well as protection from the environment and predation. This ubiquitous yet evolutionarily variable feature has been instrumental in facilitating the adoption of a variety of lifestyles and the exploitation of ecological niches across all environments. Throughout the radiation that produced the more than one million described modern species, adaptability afforded by segmentation and exoskeletons has led to a diversity that is unrivalled amongst animals. However, because of the limited extensibility of exoskeleton chitin and cuticle components, they must be periodically shed and replaced with new larger ones, notably to accommodate the growing individuals encased within. Therefore, arthropods grow discontinuously by undergoing periodic moulting events, which follow a series of steps from the preparatory pre-moult phase to ecdysis itself and post-moult maturation of new exoskeletons. Each event represents a particularly vulnerable period in an arthropod's life cycle, so processes must be tightly regulated and meticulously executed to ensure successful transitions for normal growth and development. Decades of research in representative arthropods provide a foundation of understanding of the mechanisms involved. Building on this, studies continue to develop and test hypotheses on the presence and function of molecular components, including neuropeptides, hormones, and receptors, as well as the so-called early, late, and fate genes, across arthropod diversity. Here, we review the literature to develop a comprehensive overview of the status of accumulated knowledge of the genetic toolkit governing arthropod moulting. From biosynthesis and regulation of ecdysteroid and sesquiterpenoid hormones, to factors involved in hormonal stimulation responses and exoskeleton remodelling, we identify commonalities and differences, as well as highlighting major knowledge gaps, across arthropod groups. We examine the available evidence supporting current models of how components operate together to prepare for, execute, and recover from ecdysis, comparing reports from Chelicerata, Myriapoda, Crustacea, and Hexapoda. Evidence is generally highly taxonomically imbalanced, with most reports based on insect study systems. Biases are also evident in research on different moulting phases and processes, with the early triggers and late effectors generally being the least well explored. Our synthesis contrasts knowledge based on reported observations with reasonably plausible assumptions given current taxonomic sampling, and exposes weak assumptions or major gaps that need addressing. Encouragingly, advances in genomics are driving a diversification of tractable study systems by facilitating the cataloguing of putative genetic toolkits in previously under-explored taxa. Analysis of genome and transcriptome data supported by experimental investigations have validated the presence of an "ultra-conserved" core of arthropod genes involved in moulting processes. The molecular machinery has likely evolved with elaborations on this conserved pathway backbone, but more taxonomic exploration is needed to characterise lineage-specific changes and novelties. Furthermore, linking these to transformative innovations in moulting processes across Arthropoda remains hampered by knowledge gaps and hypotheses based on untested assumptions. Promisingly however, emerging from the synthesis is a framework that highlights research avenues from the underlying genetics to the dynamic molecular biology through to the complex physiology of moulting.
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Affiliation(s)
- Giulia Campli
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Olga Volovych
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Kenneth Kim
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Werner P Veldsman
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Harriet B Drage
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Idan Sheizaf
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sinéad Lynch
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Ariel D Chipman
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Allison C Daley
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
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Yang X, Chen X, Liu C, Wang Z, Lei W, Li Q, Zhao Y, Wang X. Dynamic Alternative Polyadenylation during Litopenaeus Vannamei Metamorphosis Development. Genes (Basel) 2024; 15:837. [PMID: 39062616 PMCID: PMC11275414 DOI: 10.3390/genes15070837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
As an important mechanism in the post-transcriptional regulation of eukaryotic gene expression, alternative polyadenylation (APA) plays a key role in biological processes such as cell proliferation and differentiation. However, the role and dynamic pattern of APA during Litopenaeus vannamei metamorphosis are poorly understood. Here, RNA-seq data covering from the embryo to the maturation (16 time points) of L. vannamei were utilized. We identified 247 differentially expressed APA events between early and adult stages, and through fuzzy mean clustering analysis, we discovered five dynamic APA patterns. Among them, the gradual elongation of the 3'UTR is the major APA pattern that changes over time, and its genes are enriched in the pathways of protein and energy metabolism. Finally, we constructed mRNA-miRNA and PPI networks and detected several central miRNAs that may regulate L. vannamei development. Our results revealed the complex APA mechanisms in L. vannamei metamorphosis, shedding new light on post-transcriptional regulation of crustacean metamorphosis.
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Affiliation(s)
- Xueqin Yang
- China (Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (X.Y.); (X.C.)
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
| | - Xiuli Chen
- China (Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (X.Y.); (X.C.)
- Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China;
| | - Chengzhang Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
| | - Zezhong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
| | - Wei Lei
- Department of Pharmaceutical and Graduate Life Sciences, College of Pharmacy, Natural & Health Sciences, Manchester University, Fort Wayne, IN 46845, USA;
| | - Qiangyong Li
- Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China;
| | - Yongzhen Zhao
- China (Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (X.Y.); (X.C.)
- Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China;
| | - Xia Wang
- China (Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (X.Y.); (X.C.)
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
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Tong D, Yu Y, Lu L, Zhou W, Yu Y, Zhang X, Tian D, Liu G, Shi W. Microplastics weaken the exoskeletal mechanical properties of Pacific whiteleg shrimp Litopenaeus vannamei. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133771. [PMID: 38364581 DOI: 10.1016/j.jhazmat.2024.133771] [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: 12/12/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024]
Abstract
The ubiquitous presence of microplastics (MPs) in aquatic environments poses a significant threat to crustaceans. Although exoskeleton quality is critical for crustacean survival, the impact of MPs on crustacean exoskeletons remains elusive. Our study represents a pioneering effort to characterize the effects of MPs exposure on crustacean exoskeletons. In this study, the mechanical properties of whiteleg shrimp Litopenaeus vannamei exoskeletons were analyzed after exposure to environmentally realistic levels of MPs. Nanoindentation data demonstrated that MPs exposure significantly increased the hardness and modulus of both the carapace and abdominal segments of L. vannamei. Moreover, fractures and embedded MPs were detected on the exoskeleton surface using SEM-EDS analysis. Further analysis demonstrated that the degree of chitin acetylation (DA) in the shrimp exoskeleton, as indicated by FTIR peaks, was reduced by MPs exposure. In addition, exposure to MPs significantly inhibited the muscle Ca2+-ATPase activity and hemolymph calcium levels. Transcriptome and metabolome analyses revealed that the expression levels of genes encoding key enzymes and metabolites in the chitin biosynthetic pathway were significantly affected by MPs exposure. In conclusion, MPs at environmentally relevant concentrations may affect the exoskeletal mechanical properties of L. vannamei through a comprehensive mechanism involving the disruption of the crystalline structure of chitin, assimilation into the exoskeleton, and dysregulation of exoskeleton biosynthesis-related pathways.
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Affiliation(s)
- Difei Tong
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yingying Yu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Lingzheng Lu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yihan Yu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xunyi Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Dandan Tian
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China.
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Flores-Chavarria A, Rodríguez-Jaramillo C, Band-Schmidt CJ, Hernández-Sandoval FE, Núñez-Vázquez E, Bustillos-Guzmán JJ. Effect of dissolved metabolites of the dinoflagellate Gymnodinium catenatum (Graham, 1943) on the white shrimp Litopenaeus vannamei (Boone, 1931): A histological study. Heliyon 2023; 9:e17018. [PMID: 37484312 PMCID: PMC10361116 DOI: 10.1016/j.heliyon.2023.e17018] [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: 10/06/2022] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 07/25/2023] Open
Abstract
Harmful algae blooms (HABs) are a conspicuous phenomenon that affect the coastal zone worldwide. Aquaculture industry zones are not excluded from being affected by HAB that cause organism mortality and jeopardize their innocuity due to the contamination by phytotoxins with the concomitant economic losses. Direct ingestion of metabolites from HAB species or organisms contaminated with phycotoxins together with dermal absorption of dissolved metabolites (DM), including toxins, are the two main routes of poisoning. From these poisoning routes, the effect of DM, particularly paralytic shellfish toxins (PST), has been relatively understudied. This intoxication route can be conspicuous and could be involved in many significant mortalities of cultivated marine organisms. In this study, white shrimp juveniles (2.1 g wet weight) of Litopenaeus vannamei were exposed to extracts of 104, 105 and 106 cells/L of the dinoflagellate Gymnodinium catenatum, a PST producer. The experiment ended after 17 h of exposure when shrimps exposed to 106 cells/L extract started to die and the rest of the shrimps, from this and other treatments, did not respond to gentle physical stimulus and their swimming activity was low and erratic. Toxin concentrations were determined using high performance liquid chromatography while qualitative and quantitative histological damages were assessed on the tissues. In general, most toxins were accumulated in the hepatopancreas where more than 90% were found. Other tissues such as intestine, muscle, and gills contained less than 10% of toxins. Compared to the control, the main significative tissue damages were, loss of up to 80% of the nerve cord, 40% of the muscle coverage area, and reduction of the gill lamella width. Also, atrophy in hepatopancreas was observed, manifested by a decrease in the height of B cells, lumen degeneration and thinning of tubules. Some damages were more evident when shrimps were exposed to higher concentrated extracts of G. catenatum, however, not all damages were progressive and proportional to the extract concentration. These data confirm that PST dissolved enter the shrimp, possibly via the gills, and suggest that dissolved metabolites, including PST, may cause tissue damage. Other dissolved metabolites produced by G. catenatum, alone or in synergy, may also be involved. These results also pointed out the importance of dissolved molecules produced for this dinoflagellate and the potential effect on cultured shrimp.
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Affiliation(s)
- A.M. Flores-Chavarria
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, B.C.S., Mexico
| | - Carmen Rodríguez-Jaramillo
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, B.C.S., Mexico
| | - Christine J. Band-Schmidt
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Ave. Instituto Politécnico Nacional s/n, Col. Playa Palo de Santa Rita, C.P. 23096, La Paz, B.C.S., Mexico
| | - Francisco E. Hernández-Sandoval
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, B.C.S., Mexico
| | - Erick Núñez-Vázquez
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, B.C.S., Mexico
| | - José J. Bustillos-Guzmán
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, B.C.S., Mexico
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Mendoza-Porras O, Broadbent JA, Beale DJ, Escobar-Correas SM, Osborne SA, Simon CJ, Wade NM. Post-prandial response in hepatopancreas and haemolymph of Penaeus monodon fed different diets. Omics insights into glycoconjugate metabolism, energy utilisation, chitin biosynthesis, immune function, and autophagy. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY PART D: GENOMICS AND PROTEOMICS 2023; 46:101073. [PMID: 37018937 DOI: 10.1016/j.cbd.2023.101073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023]
Abstract
Raw materials or bioactive ingredients trigger mechanisms to assimilate nutrients and activate metabolic pathways that promote growth, immune function, or energy storage. Our understanding of these processes at a molecular level remains limited in aquaculture, especially in shrimp. Here, hepatopancreas proteomics and haemolymph metabolomics were used to investigate the post-prandial response of black tiger shrimps (Penaeus monodon) fed a conventional fishmeal diet (FM); a diet supplemented with the microbial biomass Novacq™ (NV); krill meal (KM); or, fasted (FS). Using FM as a control, a 2-fold change in abundance threshold was implemented to determine the significance of proteins and metabolites. NV fed shrimp showed preference for energy derived from carbohydrates indicated by a strong signature of glycoconjugate metabolism and activation of the amino- and nucleotide sugar metabolic pathway. KM activated the glyoxylate and dicarboxylate pathway that denoted shrimp preference for lipidic energy. KM also influenced energy generation by the TCA cycle inferred from higher abundance of the metabolites succinic semialdehyde, citric acid, isocitrate, alpha ketoglutarate and ATP and downregulation of the enzyme isocitrate dehydrogenase that catalyses oxidative decarboxylation of isocitrate. FS shrimp displayed down-regulation of oxidative phosphorylation and resorted to internal lipid reserves for energy homeostasis displaying a strong signature of autophagy. Pyrimidine metabolism was the preferred energy strategy in this group. Our study also provided evidence that during fasting or consumption of specific ingredients, shrimp share common pathways to meet their energy requirements, however, the intensity at which these pathways were impacted was diet dependent.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia.
| | - James A Broadbent
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - David J Beale
- CSIRO Land and Water, Ecosciences Precinct, Dutton Park, QLD, Australia
| | | | - Simone A Osborne
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Cedric J Simon
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Nicholas M Wade
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
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Transcriptomic analysis of the black tiger shrimp (Penaeus monodon) reveals insights into immune development in their early life stages. Sci Rep 2021; 11:13881. [PMID: 34230553 DOI: 10.1038/s41598-021-93364-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
With the rapid growth in the global demand, the shrimp industry needs integrated approaches for sustainable production. A high-quality shrimp larva is one of the crucial key requirements to maximize shrimp production. Survival and growth rates during larval development are often criteria to evaluate larval quality, however many aspects of gene regulation during shrimp larval development have not yet been identified. To further our understanding of biological processes in their early life, transcriptomic analysis of larval developmental stages (nauplius, zoea, mysis, and postlarva) were determined in the black tiger shrimp, Penaeus monodon using next-generation RNA sequencing. Gene clustering and gene enrichment analyses revealed that most of the transcripts were mainly related to metabolic processes, cell and growth development, and immune system. Interestingly, Spätzle and Toll receptors were found in nauplius stage, providing evidence that Toll pathway was a baseline immune system established in early larval stages. Genes encoding pathogen pattern-recognition proteins (LGBP, PL5-2 and c-type lectin), prophenoloxidase system (PPAE2, PPAF2 and serpin), antimicrobial peptides (crustin and antiviral protein), blood clotting system (hemolymph clottable protein) and heat shock protein (HSP70) were expressed as they developed further, suggesting that these immune defense mechanisms were established in later larval stages.
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Uengwetwanit T, Pootakham W, Nookaew I, Sonthirod C, Angthong P, Sittikankaew K, Rungrassamee W, Arayamethakorn S, Wongsurawat T, Jenjaroenpun P, Sangsrakru D, Leelatanawit R, Khudet J, Koehorst JJ, Schaap PJ, Martins dos Santos V, Tangy F, Karoonuthaisiri N. A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. Mol Ecol Resour 2021; 21:1620-1640. [PMID: 33586292 PMCID: PMC8197738 DOI: 10.1111/1755-0998.13357] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 01/31/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.
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Affiliation(s)
- Tanaporn Uengwetwanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wirulda Pootakham
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Chutima Sonthirod
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Pacharaporn Angthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Kanchana Sittikankaew
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wanilada Rungrassamee
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Sopacha Arayamethakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Duangjai Sangsrakru
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Rungnapa Leelatanawit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Jutatip Khudet
- Shrimp Genetic Improvement CenterIntegrative Aquaculture Biotechnology Research GroupSurat ThaniThailand
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Frédéric Tangy
- Viral Genomics and Vaccination UnitUMR3569 CNRSVirology DepartmentInstitut PasteurParisFrance
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
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Molecular characterization and function of chitin deacetylase-like from the Chinese mitten crab, Eriocheir sinensis. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110612. [PMID: 33992769 DOI: 10.1016/j.cbpb.2021.110612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022]
Abstract
Chitin deacetylases are essential enzymes in the chitin-modifying process and play vital roles in arthropod molting. In this study, we identified and characterized a chitin deacetylase-like (EsCDA-l) gene in the Chinese mitten crab, Eriocheir sinensis. The open reading frame of EsCDA-l was 2555 bp and encoded 554 amino acid residues that contained typical domain structure of carbohydrate esterase family 4. Phylogenetic analysis reveal that EsCDA-l belongs to the group I chitin deacetylase family. Quantitative real-time PCR analyses showed that EsCDA-l was highly expressed in exoskeletal tissues and megalopa stages. During the molting cycle, EsCDA-l was up-regulated periodically in the post-molt stage. Knockdown of EsCDA-l resulted in the abnormal ultrastructure of cuticle, prevented molting to high mortality suggesting EsCDA-l is indispensable for molting. The characterization and function analysis of the EsCDA-l should provide useful reference for further research on the utility of key genes involved in the chitin metabolic pathway in the molting process of the Chinese mitten crab as well as other crustaceans.
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9
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Huang YY, Wang GD, Liu JS, Zhang LL, Huang SY, Wang YL, Yang ZW, Ge H. Analysis of transcriptome difference between rapid-growing and slow-growing in Penaeus vannamei. Gene 2021; 787:145642. [PMID: 33848570 DOI: 10.1016/j.gene.2021.145642] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/28/2021] [Accepted: 04/07/2021] [Indexed: 01/13/2023]
Abstract
Penaeus vannamei is the principle cultured shrimp species in China. However, with the increase of culture density, the growth difference between individuals is also expanding. Here, we make use of RNA-seq to study the growth mechanisms of P. vannamei. After 120 days, we examined the transcriptomes of rapid-growing individuals (RG) and slow-growing individuals (SG). A total of 2116 and 176 differentially expressed genes (DEGs) were found in SG and RG, respectively. Moreover, the main DEGs are opsin, heat shock protein (HSP), actin, myosin, superoxide dismutase (SOD), cuticle protein, and chitinase. GO analysis further revealed that the DEGs were enriched in biological processes significantly, such as "sensory perception," "sensory perception of light stimulus," "response to stimulus," and "response to stress." Additionally, KEGG enrichment analysis showed that the DEGs were mainly enriched in "pentose and glucuronate interconversions," "amino sugar and nucleotide sugar metabolism," "glycophospholipid biosynthesis," and "glutathione metabolism." Interestingly, the upstream genes in the ecdysone signaling pathway, including molting inhibition hormone (MIH) and crustacean hyperglycemic hormone (CHH), did not differ significantly between RG and SG, which suggests that the cause for the inconsistent growth performance is due to the stress levels rather than the ecdysone signal pathway. In summary, this work provides data that will be useful for future studies on shrimp growth and development.
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Affiliation(s)
- Yong-Yu Huang
- Fisheries College of Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Guo-Dong Wang
- Fisheries College of Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China.
| | - Jun-Sheng Liu
- Fisheries College of Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Li-Li Zhang
- Fisheries College of Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Shi-Yu Huang
- Fisheries College of Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Yi-Lei Wang
- Fisheries College of Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Zhang-Wu Yang
- Fisheries Research Institute of Fujian, 7 Shanhai Road, Huli, Xiamen 361000, China.
| | - Hui Ge
- Fisheries Research Institute of Fujian, 7 Shanhai Road, Huli, Xiamen 361000, China
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10
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Yuan H, Zhang W, Fu Y, Jiang S, Xiong Y, Zhai S, Gong Y, Qiao H, Fu H, Wu Y. MnFtz-f1 Is Required for Molting and Ovulation of the Oriental River Prawn Macrobrachium nipponense. Front Endocrinol (Lausanne) 2021; 12:798577. [PMID: 34987481 PMCID: PMC8721877 DOI: 10.3389/fendo.2021.798577] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Molting and ovulation are the basic processes responsible for the growth and reproduction of Macrobrachium nipponense; however, the molecular mechanisms of molting and ovulation in M. nipponense are poorly understood. The present study aimed to use MnFtz-f1 as the starting point to study the molting and ovulation phenomena in M. nipponense at the molecular level. The full-length MnFtz-f1 cDNA sequence was 2,198 base pairs (bp) in length with an open reading frame of 1,899 bp encoding 632 amino acids. Quantitative real-time PCR analysis showed that MnFtz-f1 was highly expressed in the ovary at the cleavage stage and on the fifth day after hatching. In vivo administration of 20-hydroxyecdysone (20E) showed that 20E effectively inhibited the expression of the MnFtz-f1 gene, and the silencing of the MnFtz-f1 gene reduced the content of 20E in the ovary. In situ hybridization (ISH) analysis revealed the localization of MnFtz-f1 in the ovary. Silencing of MnFtz-f1 by RNA interference (RNAi) resulted in significant inhibition of the expression of the vitellogenin (Vg), Spook, and Phantom genes, thus confirming that MnFtz-f1 had a mutual regulatory relationship with Vg, Spook, and Phantom. After RNAi, the molting frequency and ovulation number of M. nipponense decreased significantly, which demonstrated that MnFtz-f1 played a pivotal role in the process of molting and ovulation.
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Affiliation(s)
- Huwei Yuan
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yin Fu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Shuhua Zhai
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yongsheng Gong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- *Correspondence: Hui Qiao, ; Hongtuo Fu,
| | - Hongtuo Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- *Correspondence: Hui Qiao, ; Hongtuo Fu,
| | - Yan Wu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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11
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Wang J, Chen X, He F, Song X, Huang S, Yue W, Chen Y, Su Z, Wang C. Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:443-454. [PMID: 33346084 PMCID: PMC8242267 DOI: 10.1016/j.gpb.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/04/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs, and adult crabs) and different tissues (eyestalk, hepatopancreas, and muscle from juvenile crabs, and eyestalk, hepatopancreas, muscle, heart, stomach, gill, thoracic ganglia, intestine, ovary, and testis from adult crabs) of E. sinensis. A comprehensive reference transcriptome was assembled, including 19,023 protein-coding genes. Hierarchical clustering based on 128 differentially expressed cuticle-related genes revealed two distinct expression patterns during the early larval developmental stages, demonstrating the distinct roles of these genes in “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting. Phylogenetic analysis of 1406 one-to-one orthologous gene families identified from seven arthropod species and Caenorhabditis elegans strongly supported the hypothesis that Malacostraca and Branchiopoda do not form a monophyletic group. Furthermore, Branchiopoda is more phylogenetically closely related to Hexapoda, and the clade of Hexapoda and Branchiopoda and the clade of Malacostraca belong to the Pancrustacea. This study offers a high-quality transcriptome resource for E. sinensis and demonstrates the evolutionary relationships of major arthropod groups. The differentially expressed genes identified in this study facilitate further investigation of the cuticle-related gene expression networks which are likely associated with “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Xiaowen Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Funan He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao Song
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Shu Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Wucheng Yue
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yipei Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhixi Su
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China.
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12
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Rojo-Arreola L, García-Carreño F, Romero R, Díaz Dominguez L. Proteolytic profile of larval developmental stages of Penaeus vannamei: An activity and mRNA expression approach. PLoS One 2020; 15:e0239413. [PMID: 32946520 PMCID: PMC7500676 DOI: 10.1371/journal.pone.0239413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/05/2020] [Indexed: 11/18/2022] Open
Abstract
In arthropods, the cleavage of specific proteins by peptidases has pivotal roles in multiple physiological processes including oogenesis, immunity, nutrition, and parasitic infection. These enzymes are also key players in the larval development, and well-described triggers of molting and metamorphosis. In this work the peptidase complement throughout the larvae development of Penaeus vannamei was quantified at the transcript and activity level using qPCR and fluorogenic substrates designed to be hydrolyzed by class-specific peptidases respectively, providing a detailed identification of the proteolytic repertoire in P. vannamei larvae. Significant changes in the peptidase activity profile were observed. During the lecithotrophic naupliar instars, the dominant peptidase activity and expression derive from cysteine peptidases, suggesting that enzymes of this class hydrolyze the protein components of yolk as the primary amino acid source. At the first feeding instar, zoea, dominant serine peptidase activity was found where trypsin activity is particularly high, supporting previous observations that during zoea the breakdown of food protein is primarily enzymatic. At decapodid stages the peptidase expression and activity is more diverse indicating that a multienzyme network achieves food digestion. Our results suggest that proteolytic enzymes fulfill specific functions during P. vannamei larval development.
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Affiliation(s)
| | | | - Rogelio Romero
- Centro de Investigaciones Biológicas del Noroeste, México City, México
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13
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Zhang X, Yuan J, Zhang X, Xiang J, Li F. Genomic Characterization and Expression of Juvenile Hormone Esterase-Like Carboxylesterase Genes in Pacific White Shrimp, Litopenaeus vannamei. Int J Mol Sci 2020; 21:ijms21155444. [PMID: 32751646 PMCID: PMC7432913 DOI: 10.3390/ijms21155444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/02/2022] Open
Abstract
The sesquiterpenoid methyl farnesoate (MF), a juvenile hormone (JH) analog, plays important roles in many physiological processes of crustaceans, such as morphogenesis, molting and reproduction. Juvenile hormone esterase-like (JHE-like) carboxylesterase (CXE) is a key enzyme in MF degradation, playing a significant role in regulating MF titer. However, its function is barely known in shrimp. In this study, a total of 21 JHE-like CXEs (LvCXEs) were characterized in Pacific white shrimp Litopenaeus vannamei, based on the full genome and multi-transcriptomic data. LvCXE has a conserved triplet catalytic site (Ser-Glu-His) and a characteristic GxSxG motif. Most LvCXEs were highly expressed in the hepatopancreas, which was the main site for MF degradation. LvCXEs containing a GESAG motif showed a specific expansion in the L. vannamei genome. Those GESAG-containing LvCXEs presented differential expressions at different larvae stages and different molting stages of L. vannamei, which suggested their potential functions in development and molting. Additionally, when the transcription level of CXEs was inhibited, it could lead to failed molt and death of L. vannamei. When we further detected the expression levels of the key ecdysone responsive transcription factors including LvE75, LvBr-C, LvHr3 and LvFtz-f1 after the CXE inhibitor was injected into L. vannamei, they all showed apparent down-regulation. These results suggested that the expansion of LvCXEs in the L. vannamei genome should contribute to the regulation of metamorphosis at larvae stages and frequent molting during the growth of L. vannamei.
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Affiliation(s)
- Xiaoxi Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbo Yuan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: (J.Y.); (X.Z.)
| | - Xiaojun Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: (J.Y.); (X.Z.)
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fuhua Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (F.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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14
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Van Quyen D, Gan HM, Lee YP, Nguyen DD, Nguyen TH, Tran XT, Nguyen VS, Khang DD, Austin CM. Improved genomic resources for the black tiger prawn (Penaeus monodon). Mar Genomics 2020; 52:100751. [PMID: 32033920 DOI: 10.1016/j.margen.2020.100751] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/24/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022]
Abstract
World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general lack of genomic resources available for shrimp species, which is challenging to obtain due to the need to deal with large repetitive genomes, which characterize many decapod crustaceans. The first tiger prawn (P. monodon) genome assembly was assembled in 2016 using the standard Illumina PCR-based pair-end reads and a computationally-efficient but relatively suboptimal assembler, SOAPdenovo v2. As a result, the current P. monodon draft genome is highly fragmented (> 2 million scaffolds with N50 length of <1000 bp), exhibiting only moderate genome completeness (< 35% BUSCO complete single-copy genes). We sought to improve upon the recently published P. monodon genome assembly and completeness by generating Illumina PCR-free pair-end sequencing reads to eliminate genomic gaps associated with PCR-bias and performing de novo assembly using the updated MaSurCA de novo assembler. Furthermore, we scaffolded the assembly with low coverage Nanopore long reads and several recently published deep Illumina transcriptome paired-end sequencing data, producing a final genome assembly of 1.6 Gbp (1,211,364 scaffolds; N50 length of 1982 bp) with an Arthropod BUSCO completeness of 96.8%. Compared to the previously published P. monodon genome assembly from China (NCBI Accession Code: NIUS01), this represents an almost 20% increase in the overall BUSCO genome completeness that now consists of more than 90% of Arthropod BUSCO single-copy genes. The revised P. monodon genome assembly (NCBI Accession Code: VIGR01) will be a valuable resource to support ongoing functional genomics and molecular-based breeding studies in Vietnam.
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Affiliation(s)
- Dong Van Quyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam; University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia; Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia; Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Dinh Duy Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Thi Hoa Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Xuan Thach Tran
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam
| | - Van Sang Nguyen
- Institute for Aquaculture No.2 (RIA2), 116 Nguyen Dinh Chieu St., Dist. 1, Ho Chi Minh City, Viet Nam
| | - Dinh Duy Khang
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam.
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia; Deakin Genomics Centre, Deakin University, Geelong, Australia.
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15
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Drozdova P, Rivarola-Duarte L, Bedulina D, Axenov-Gribanov D, Schreiber S, Gurkov A, Shatilina Z, Vereshchagina K, Lubyaga Y, Madyarova E, Otto C, Jühling F, Busch W, Jakob L, Lucassen M, Sartoris FJ, Hackermüller J, Hoffmann S, Pörtner HO, Luckenbach T, Timofeyev M, Stadler PF. Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods. BMC Genomics 2019; 20:712. [PMID: 31519144 PMCID: PMC6743106 DOI: 10.1186/s12864-019-6024-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Background Lake Baikal is one of the oldest freshwater lakes and has constituted a stable environment for millions of years, in stark contrast to small, transient bodies of water in its immediate vicinity. A highly diverse endemic endemic amphipod fauna is found in one, but not the other habitat. We ask here whether differences in stress response can explain the immiscibility barrier between Lake Baikal and non-Baikal faunas. To this end, we conducted exposure experiments to increased temperature and the toxic heavy metal cadmium as stressors. Results Here we obtained high-quality de novo transcriptome assemblies, covering mutiple conditions, of three amphipod species, and compared their transcriptomic stress responses. Two of these species, Eulimnogammarus verrucosus and E. cyaneus, are endemic to Lake Baikal, while the Holarctic Gammarus lacustris is a potential invader. Conclusions Both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions. Electronic supplementary material The online version of this article (10.1186/s12864-019-6024-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Polina Drozdova
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Lorena Rivarola-Duarte
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.,Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Seeland OT Gatersleben, D-06466, Germany.,Plant Genome and Systems Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, D-85764, Germany
| | - Daria Bedulina
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Denis Axenov-Gribanov
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Stephan Schreiber
- Young Investigator Group Bioinformatics & Transcriptomics, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Anton Gurkov
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Zhanna Shatilina
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Kseniya Vereshchagina
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Yulia Lubyaga
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Ekaterina Madyarova
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Christian Otto
- ecSeq Bioinformatics GmbH, Sternwartenstraße 29, Leipzig, D-04103, Germany
| | - Frank Jühling
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 3 Rue Koeberlé, Strasbourg, F-67000, France.,Université de Strasbourg, 4 Rue Blaise Pascal, Strasbourg, F-67000, France
| | - Wibke Busch
- Department of Bioanalytical Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Lena Jakob
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Magnus Lucassen
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Franz Josef Sartoris
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Jörg Hackermüller
- Young Investigator Group Bioinformatics & Transcriptomics, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Steve Hoffmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Hans-Otto Pörtner
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, D-27570, Germany
| | - Till Luckenbach
- Department of Bioanalytical Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, D-04318, Germany
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, Lenin str. 3, Irkutsk, RUS-664025, Russia.,Baikal Research Centre, Lenin str. 21, Irkutsk, RUS-664025, Russia
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany. .,Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090, Austria. .,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, D.C., COL-111321, Colombia. .,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA.
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16
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Li J, Sun J, Dong X, Geng X, Qiu G. Transcriptomic analysis of gills provides insights into the molecular basis of molting in Chinese mitten crab ( Eriocheir sinensis). PeerJ 2019; 7:e7182. [PMID: 31293829 PMCID: PMC6601604 DOI: 10.7717/peerj.7182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/23/2019] [Indexed: 01/31/2023] Open
Abstract
Chinese mitten crab (Eriocheir sinensis) is an economically important freshwater aquaculture species and is a model species for research on the mechanism of molting. This study aimed to identify important candidate genes associated with the molting process and to determine the role of gills in the regulation of molting with the help of transcriptomic analysis. The transcriptomes of crabs at different molting stages—postmolt (PoM), intermolt (InM), premolt (PrM) and ecdysis (E)—were de novo assembled to generate 246,232 unigenes with a mean length of 851 bp. A total of 86,634 unigenes (35.18% of the total unigenes) were annotated against reference databases. Significantly upregulated genes were identified in postmolt compared to intermolt (1,475), intermolt compared to premolt (65), premolt compared to ecdysis (1,352), and ecdysis compared to postmolt (153), and the corresponding numbers of downregulated genes were 1,276, 32, 1,573 and 171, respectively. Chitin synthase, endochitinase, chitinase A, chitinase 3, chitinase 6 and chitin deacetylase 1 were upregulated during the postmolt and ecdysis stages, while phosphoglucomutase 3 (PGM3), glucosamine 6-phosphate deaminase (GNPDA) and glucosamine glycoside hydrolase (nagZ) were upregulated during the intermolt and premolt stages compared to the other stages. The upregulated genes were enriched in several lipid-related metabolic pathways, such as “fatty acid elongation”, “glycerophospholipid metabolism” and “sulfur metabolism”. Meanwhile, three signaling pathways, including the “phosphatidylinositol signaling system”, the “calcium signaling pathway” and the “GnRH signaling pathway” were also enriched. Tetraspanin-18, an important effector gene in the lysosomal pathway involved in cell apoptosis, up-regulate with the beginning of molting (in premolt stage) and reach the top in the ecdysis stage, and barely expressed in the intermolt stage. The expression variations in the tetraspanin-18 gene indicated that it may play an important role in the beginning of molting cycle, which might be regulated by the stress of salinity. This study revealed that the gills could participate in chitin degradation, in reestablishment of the exoskeleton and the signaling process. Based on transcriptomic analysis of the gills, we not only explored novel molecular mechanisms of molting in E. sinensis but also acquired foundational genetic data for E. sinensis.
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Affiliation(s)
- Jingjing Li
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China.,Tianjin Diseases Prevention and Control Center of Aquatic Animals, Tianjin, China
| | - Jinsheng Sun
- Tianjin Key Laboratory for Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Xuewang Dong
- Tianjin Diseases Prevention and Control Center of Aquatic Animals, Tianjin, China
| | - Xuyun Geng
- Tianjin Diseases Prevention and Control Center of Aquatic Animals, Tianjin, China
| | - Gaofeng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
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17
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Wang Z, Luan S, Meng X, Cao B, Luo K, Kong J. Comparative transcriptomic characterization of the eyestalk in Pacific white shrimp (Litopenaeus vannamei) during ovarian maturation. Gen Comp Endocrinol 2019; 274:60-72. [PMID: 30611813 DOI: 10.1016/j.ygcen.2019.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 12/17/2022]
Abstract
In crustaceans, some of fundamental regulatory processes related to a range of physiological functions, including ovarian maturation, molting, glucose homeostasis, osmoregulation, etc., occur in the organs of the eyestalk. Additionally, reproduction is regulated by neuropeptide hormones and other proteins released from secretory sites (X-organ/sinus gland, XO/SG) within the eyestalk. As unilateral eyestalk ablation was the most common method used to artificially induce ovarian maturation for farmed Litopenaeus vannamei, to better understand the reproductive regulation mechanism in L. vannamei, we have investigated the transcriptomes of the eyestalk during five ovary developmental stages with or without eyestalk ablation by high-throughput Illumina sequencing technology. The raw reads were assembled and clustered into 127,031 unigenes. Meanwhile, the differentially expressed genes (DEGs) between ovarian development stages were identified. We examined, through DEG enrichment analysis, eyestalk gene expression patterns for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, comparing natural to artificially induced ovarian maturation. We also identified a variety of transcripts that appear to be differentially expressed throughout ovarian maturation. These include transcripts that encode G-protein coupled receptors (GPCRs) and neuropeptides, such as the crustacean hyperglycemic hormone (CHH), molt-inhibiting hormone (MIH), and crustacean female sex hormone (CFSH). Furthermore, numerous exoskeleton formation-related genes were found to be down-regulated during ovarian maturation, including cuticle-like proteins, eclosion hormone (EH), and gastrolith-like proteins, of which the latter are the first reported in L. vannamei. Our work is the first reproduction-related investigation of L. vannamei focusing on the eyestalk at the whole transcriptome level. These findings provide novel insight into the function of the eyestalk in reproduction regulation.
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Affiliation(s)
- Zhongkai Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Sheng Luan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Xianhong Meng
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Baoxiang Cao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Kun Luo
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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18
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Zhang X, Yuan J, Sun Y, Li S, Gao Y, Yu Y, Liu C, Wang Q, Lv X, Zhang X, Ma KY, Wang X, Lin W, Wang L, Zhu X, Zhang C, Zhang J, Jin S, Yu K, Kong J, Xu P, Chen J, Zhang H, Sorgeloos P, Sagi A, Alcivar-Warren A, Liu Z, Wang L, Ruan J, Chu KH, Liu B, Li F, Xiang J. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nat Commun 2019; 10:356. [PMID: 30664654 PMCID: PMC6341167 DOI: 10.1038/s41467-018-08197-4] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/07/2018] [Indexed: 01/08/2023] Open
Abstract
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture. The Pacific white shrimp Litopenaeus vannamei is an important aquaculture species and a promising model for crustacean biology. Here, the authors provide a reference genome assembly, and show that gene expansion is involved in the regulation of frequent molting as well as benthic adaptation of the shrimp.
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Affiliation(s)
- Xiaojun Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jianbo Yuan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yamin Sun
- Tianjin Biochip Corporation, Tianjin, 300457, China
| | - Shihao Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yi Gao
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Yu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chengzhang Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Quanchao Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xinjia Lv
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ka Yan Ma
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., 999077, Hong Kong SAR
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wenchao Lin
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Long Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xueli Zhu
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chengsong Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jiquan Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Songjun Jin
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Kuijie Yu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Peng Xu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Jack Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Hongbin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Patrick Sorgeloos
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Amir Sagi
- Department of Life Sciences and the National Institute for Biotechnology, Negev Ben Gurion University, Beer Sheva, 84105, Israel
| | | | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lei Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., 999077, Hong Kong SAR.
| | - Bin Liu
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Fuhua Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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19
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018; 43:189-223. [PMID: 29485126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains.
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Affiliation(s)
- Gunter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany,
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20
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018. [DOI: 10.1007/s12038-018-9741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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