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Dourdin TS, Berthelin C, Guyomard K, Morin A, Morandi N, Elie N, Villain-Naud N, Rivière G, Sussarellu R. The Pacific oyster reproduction is affected by early-life exposure to environmental pesticide mixture: A multigenerational study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173569. [PMID: 38810751 DOI: 10.1016/j.scitotenv.2024.173569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 05/31/2024]
Abstract
Pesticides threat marine organisms worldwide. Among them, the Pacific oyster is a bivalve mollusc model in marine ecotoxicology. A large body of literature already stated on the multiple-scale effects pesticides can trigger in the Pacific oyster, throughout its life cycle and in a delayed manner. In particular, reproductive toxicity is of major concern because of its influence on population dynamics. However, past studies mostly investigated pesticide reprotoxicity as a direct effect of exposure during gametogenesis or directly on gametes and little is known about the influence of an early embryo exposure on the breed capacity. Therefore, we studied delayed and multigenerational consequences through gametogenesis features (i.e. sex ratio, glycogen content, gene expression) and reproductive success in two consecutive oyster generations (F0 and F1) exposed to an environmentally-relevant pesticide mixture (sum nominal concentration: 2.85 μg.L-1) during embryo-larval development (0-48 h post fertilization, hpf). In the first generation, glycogen content increased in exposed individuals and the expression of some gametogenesis target genes was modified. The reproductive success measured 48 hpf was higher in exposed individuals. A multigenerational influence was observed in the second generation, with feminisation, acceleration of gametogenesis processes and the sex-specific modification of glycogen metabolism in individuals from exposed parents. This study is the first to highlight the delayed effects on reproduction induced by an early exposure to pesticides, and its multigenerational implications in the Pacific oyster. It suggests that environmental pesticide contamination can have impacts on the recruitment and the dynamics of natural oyster populations exposed during their embryo-larval phase.
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Affiliation(s)
- Thomas Sol Dourdin
- Ifremer, CCEM Contamination Chimique des Écosystèmes Marins, F-44000, France
| | - Clothilde Berthelin
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR8067, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231 Paris CEDEX, France
| | - Killian Guyomard
- Ifremer, EMMA Plateforme Expérimentale Mollusques Marins Atlantique, F-85230, France
| | - Alicia Morin
- Ifremer, CCEM Contamination Chimique des Écosystèmes Marins, F-44000, France
| | - Nathan Morandi
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR8067, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231 Paris CEDEX, France
| | - Nicolas Elie
- Université de Caen Normandie, Structure Federative 4207 'Normandie Oncologie', PLATON Services Unit, Virtual'His, F-14000 Caen, France
| | - Nadège Villain-Naud
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR8067, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231 Paris CEDEX, France
| | - Guillaume Rivière
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR8067, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231 Paris CEDEX, France
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2
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Sun D, Yu H, Kong L, Liu S, Xu C, Li Q. The role of DNA methylation reprogramming during sex determination and sex reversal in the Pacific oyster Crassostrea gigas. Int J Biol Macromol 2024; 259:128964. [PMID: 38219938 DOI: 10.1016/j.ijbiomac.2023.128964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/19/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024]
Abstract
DNA methylation is instrumental in vertebrate sex reversal. However, the mechanism of DNA methylation regulation regarding sex reversal in invertebrates is unclear. In this study, we used whole genome bisulfite sequencing (WGBS) to map single-base resolution methylation profiles of the Pacific oyster, including female-to-male (FMa-to-FMb) and male-to-female (MFa-to-MFb) sex reversal, as well as sex non-reversed males and females (MMa-to-MMb and FFa-to-FFb). The results showed that global DNA methylation levels increase during female-to-male sex reversals, with a particular increase in the proportion of high methylation levels (mCGs >0.75) and a decrease in the proportion of intermediate methylation levels (0.25 < mCGs <0.75). This increase in DNA methylation was mainly associated with the elevated expression of DNA methylase genes. Genome-wide methylation patterns of females were accurately remodeled to those of males after sex reversal, while the opposite was true for the male-to-female reversal. Those findings directly indicate that alterations in DNA methylation play a significant role in sex reversal in Pacific oysters. Comparative analysis of the DNA methylomes of pre- and post- sex reversal gonadal tissues (FMb-vs-FMa or MFb-vs-MFa) revealed that differentially methylated genes were mainly involved in the biological processes of sex determination or gonadal development. However critical genes such as Dmrt1, Foxl2 and Sox-like, which are involved in the putative sex determination pathway in Pacific oysters, showed almost an absence of methylation modifications, varying greatly from vertebrates. Additionally, comparative analysis of the DNA methylomes of sexual reversal and sex non-reversal (FMa-vs-FFa or MFa-vs-MMa) revealed that heat shock protein genes, such as Hsp68-like and Hsp70B, were important for the occurrence of sex reversal. These findings shed light on the epigenetic mechanisms underlying the maintenance of gonadal plasticity and the reversal of organ architecture in oysters.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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3
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Ye J, Zeng J, Zheng H, Zhang C, Zhang H, Zheng H. Genome-wide identification of STATs and analysis of their role in sex determination in Pacific oysters (Crassostrea gigas). Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110933. [PMID: 38110171 DOI: 10.1016/j.cbpb.2023.110933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
STAT (signal transducer and activator of the transcription) proteins, are a group of highly conserved transcription factors and fundamental components of the JAK-STAT signaling pathway. They play crucial roles in a variety of biological processes, such as immunity, proliferation, differentiation, and growth. However, little information is known regarding their role in gonad development and sex determination in mollusks. In this study, we identified 3 STAT genes in Pacific Oyster Crassostrea gigas. Phylogenetic analysis showed that STATs from mollusks were highly conserved, and most of them had four identical motif regions, except for the STAT1 and STAT3 predicted sequences from Crassostrea hongkongensis. Tissue expression analysis indicated CgSTAT1 had a high expression level in most tissues, while CgSTAT3 had a low expression level in most tissues. Expression analysis of early developmental stages showed CgSTAT1 had a higher expression level from egg to D shaped larva and a lower expression level in subsequent stages. In contrast CgSTAT1, CgSTAT2 had a reverse expression pattern. Expression analysis of different developmental stages of diploid gonads indicated that CgSTAT1 had a higher expression level at the S1 and S3 stages relative to the S2 stage in females, while in males the S3 stage had a higher expression than than the S2 stage. The expression level of CgSTAT1 between diploids and triploids in females differed significantly, but there were no significant differences in males. Expression of CgSTAT2 differed significantly between diploid and triploid males. These data suggest an important role for STATs in sex differentiation in diploid and triploid oysters. Our study is the first to explore the role of STATs in sex differentiation and gonadal development in oysters, and will help us better understand the molecular mechanisms of sex differentiation in shellfish.
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Affiliation(s)
- Jianming Ye
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Junxi Zeng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Haiqian Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Chuanxu Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Hongkuan Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China.
| | - Huaiping Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China.
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Sun D, Yu H, Li Q. Early gonadal differentiation is associated with the antagonistic action of Foxl2 and Dmrt1l in the Pacific oyster. Comp Biochem Physiol B Biochem Mol Biol 2023; 265:110831. [PMID: 36681266 DOI: 10.1016/j.cbpb.2023.110831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
As the second largest phylum in the zoological kingdom next to arthropods, the mechanism of gonadal differentiation in mollusca is quite complex. Currently, although much has been carried out on gonadal differentiation in the Pacific oyster, there is still unknown information that needs to be further explored. Here, analysis of the Foxl2 and Dmrt1l expression in samples at different development periods of male and female gonads as well as in annual gonad samples revealed that Log10 (Foxl2/Dmrt1l) values were an effective method for sex identification in oysters. In differentiated gonadal tissue, Log10 (Foxl2/Dmrt1l) values greater than 2 were females and less than 1 for males. Subsequent sequential sampling of the same individuals verified that Log10 (Foxl2/Dmrt1l) values greater than 2 for resting gonads would develop as females and less than 1 would develop as males in the future. Relative expression analysis of Foxl2 and Dmrt1l in the annual samples revealed a negative correlation between Log10 (Foxl2) and Log10 (Dmrt1l). Double fluorescence reporter validation results showed that DMRT1L protein was able to bind the Foxl2 promoter and repress its activity with a weak dosage effect. Antagonism between Dmrt1l and Foxl2 is therefore not restricted to vertebrates, and the competing regulatory networks are of great significance in the maintenance of gonadal sex in oysters after sexual differentiation. This study provides novel ideas and insights into the study of early gonadal differentiation in the adult oyster.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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5
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Silliman K, Spencer LH, White SJ, Roberts SB. Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate. Genome Biol Evol 2023; 15:evad013. [PMID: 36740242 PMCID: PMC10468963 DOI: 10.1093/gbe/evad013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.
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Affiliation(s)
- Katherine Silliman
- South Carolina Department of Natural Resources, Marine Resources Research
Institute, Charleston, South Carolina
| | - Laura H Spencer
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Samuel J White
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
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Venkataraman YR, White SJ, Roberts SB. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 2022; 23:556. [PMID: 35927609 PMCID: PMC9351233 DOI: 10.1186/s12864-022-08781-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/13/2022] [Indexed: 12/30/2022] Open
Abstract
Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08781-5.
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Affiliation(s)
- Yaamini R Venkataraman
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA. .,School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA.
| | - Samuel J White
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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Maillard F, Elie N, Villain-Naud N, Lepoittevin M, Martinez AS, Lelong C. Male triploid oysters of Crassostrea gigas exhibit defects in mitosis and meiosis during early spermatogenesis. FEBS Open Bio 2021; 12:1438-1452. [PMID: 34935310 PMCID: PMC9340784 DOI: 10.1002/2211-5463.13356] [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: 07/07/2021] [Revised: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 11/07/2022] Open
Abstract
The Pacific oyster, Crassostrea gigas is a successive irregular hermaphrodite mollusc which has an annual breeding cycle. Oysters are naturally diploid organisms, but triploid oysters have been developed for use in shellfish aquaculture, with the aim of obtaining sterile animals with commercial value. However, studies have shown that some triploid oysters are partially able to undergo gametogenesis, with numerous proliferating cells closed to diploids (3n alpha) or a partial one with an accumulation of locked germ cells (3n beta). The aim of our study therefore was to understand the regulation of spermatogenesis in both groups of triploid oysters (alpha and beta) from the beginning of spermatogenesis, during mitosis and meiosis events. Our results demonstrate that the reduced spermatogenesis in triploids results from a deregulation of the development of the germinal lineage and the establishment of the gonadal tract led by a lower number of tubules. Morphological cellular investigation also revealed an abnormal condensation of germ cell nuclei and the presence of clear patches in the nucleoplasm of triploid cells, which were more pronounced in beta oysters. Furthermore, studies of molecular and cellular regulation showed a downregulation of mitotic spindle checkpoint in beta oysters, resulting in disturbance of chromosomal segregation, notably on Spindle Assembly Checkpoint involved in the binding of microtubules to chromosomes. Taken together, our results suggest that the lower reproductive ability of triploid oysters may be due to cellular and molecular events such as impairment of spermatogenesis and disruptions of mitosis and meiosis, occurring early and at various stages of the gametogenetic cycle.
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Affiliation(s)
- Floriane Maillard
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Nicolas Elie
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Microscopie Appliquée à la Biologie, SF4206 Interaction Cellule-Organisme-Environnement (ICORE), Université de Caen Normandie, Esplanade de la paix, 14032, Caen CEDEX, France
| | - Nadège Villain-Naud
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Mélanie Lepoittevin
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Anne-Sophie Martinez
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Christophe Lelong
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France.,Oestrogènes et Reproduction (OeReCa), EA2608, Université de Caen Normandie, Esplanade de la paix, 14032, Caen CEDEX, France
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Broquard C, Saowaros SA, Lepoittevin M, Degremont L, Lamy JB, Morga B, Elizur A, Martinez AS. Gonadal transcriptomes associated with sex phenotypes provide potential male and female candidate genes of sex determination or early differentiation in Crassostrea gigas, a sequential hermaphrodite mollusc. BMC Genomics 2021; 22:609. [PMID: 34372770 PMCID: PMC8353863 DOI: 10.1186/s12864-021-07838-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 06/24/2021] [Indexed: 01/08/2023] Open
Abstract
Background In the animal kingdom, mollusca is an important phylum of the Lophotrochozoa. However, few studies have investigated the molecular cascade of sex determination/early gonadal differentiation within this phylum. The oyster Crassostrea gigas is a sequential irregular hermaphrodite mollusc of economic, physiological and phylogenetic importance. Although some studies identified genes of its sex-determining/−differentiating pathway, this particular topic remains to be further deepened, in particular with regard to the expression patterns. Indeed, these patterns need to cover the entire period of sex lability and have to be associated to future sex phenotypes, usually impossible to establish in this sequential hermaphrodite. This is why we performed a gonadal RNA-Seq analysis of diploid male and female oysters that have not changed sex for 4 years, sampled during the entire time-window of sex determination/early sex differentiation (stages 0 and 3 of the gametogenetic cycle). This individual long-term monitoring gave us the opportunity to explain the molecular expression patterns in the light of the most statistically likely future sex of each oyster. Results The differential gene expression analysis of gonadal transcriptomes revealed that 9723 genes were differentially expressed between gametogenetic stages, and 141 between sexes (98 and 43 genes highly expressed in females and males, respectively). Eighty-four genes were both stage- and sex-specific, 57 of them being highly expressed at the time of sex determination/early sex differentiation. These 4 novel genes including Trophoblast glycoprotein-like, Protein PML-like, Protein singed-like and PREDICTED: paramyosin, while being supported by RT-qPCR, displayed sexually dimorphic gene expression patterns. Conclusions This gonadal transcriptome analysis, the first one associated with sex phenotypes in C. gigas, revealed 57 genes highly expressed in stage 0 or 3 of gametogenesis and which could be linked to the future sex of the individuals. While further study will be needed to suggest a role for these factors, some could certainly be original potential actors involved in sex determination/early sex differentiation, like paramyosin and could be used to predict the future sex of oysters. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07838-1.
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Affiliation(s)
- Coralie Broquard
- Normandie University, UNICAEN, CNRS, BOREA, 14000, Caen, France.,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la Paix, CS 14032, 14032, Cedex 05, Caen, France.,Ifremer, RBE-SG2M-LGPMM, La Tremblade, France
| | - Suwansa-Ard Saowaros
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Mélanie Lepoittevin
- Normandie University, UNICAEN, CNRS, BOREA, 14000, Caen, France.,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la Paix, CS 14032, 14032, Cedex 05, Caen, France
| | | | | | | | - Abigail Elizur
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Anne-Sophie Martinez
- Normandie University, UNICAEN, CNRS, BOREA, 14000, Caen, France. .,Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Esplanade de la Paix, CS 14032, 14032, Cedex 05, Caen, France.
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9
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Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides. Mar Drugs 2021; 19:md19080452. [PMID: 34436291 PMCID: PMC8398477 DOI: 10.3390/md19080452] [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: 07/13/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Crassostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were de novo assembled to generate a specific reference transcriptome of the oyster nervous system and used to identify differentially expressed transcripts. Transcriptome mining led to the identification of novel neuropeptide precursors (NPPs) related to the bilaterian Eclosion Hormone (EH), crustacean female sex hormone/Interleukin 17, Nesfatin, neuroparsin/IGFBP, prokineticins, and urotensin I; to the protostome GNQQN, pleurin, prohormones 3 and 4, prothoracotropic hormones (PTTH), and QSamide/PXXXamide; to the lophotrochozoan CCWamide, CLCCY, HFAamide, and LXRX; and to the mollusk-specific NPPs CCCGS, clionin, FYFY, GNamide, GRWRN, GSWN, GWE, IWMPxxGYxx, LXRYamide, RTLFamide, SLRFamide, and WGAGamide. Among the complete repertoire of NPPs, no sex-biased expression was observed. However, 25 NPPs displayed reproduction stage-specific expression, supporting their involvement in the control of gametogenesis or associated metabolisms.
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10
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Kronberg J, Byrne JJ, Jansen J, Antczak P, Hines A, Bignell J, Katsiadaki I, Viant MR, Falciani F. Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site. Sci Rep 2021; 11:12882. [PMID: 34145300 PMCID: PMC8213754 DOI: 10.1038/s41598-021-90494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022] Open
Abstract
The monitoring of anthropogenic chemicals in the aquatic environment including their potential effects on aquatic organisms, is important for protecting life under water, a key sustainable development goal. In parallel with monitoring the concentrations of chemicals of concern, sentinel species are often used to investigate the biological effects of contaminants. Among these, bivalve molluscs such as mussels are filter-feeding and sessile, hence an excellent model system for measuring localized pollution. This study investigates the relationship between the metabolic state of the blue mussel (Mytilus edulis) and its physiology in different environments. We developed a computational model based on a reference site (relatively unpolluted) and integrated seasonal dynamics of metabolite relative concentrations with key physiological indicators and environmental parameters. The analysis of the model revealed that changes in metabolite levels during an annual cycle are influenced by water temperature and are linked to gonadal development. This work supports the importance of data-driven biology and its potential in environmental monitoring.
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Affiliation(s)
- Jaanika Kronberg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK.,Estonian Genome Centre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jonathan J Byrne
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Philipp Antczak
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Adam Hines
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - John Bignell
- Centre for Environment Fisheries and Aquaculture Science (Cefas), The North, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Ioanna Katsiadaki
- Centre for Environment Fisheries and Aquaculture Science (Cefas), The North, Barrack Road, Weymouth, Dorset, DT4 8UB, UK
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Francesco Falciani
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK.
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11
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Gallardi D, Xue X, Mercier E, Mills T, Lefebvre F, Rise ML, Murray HM. RNA-seq analysis of the mantle transcriptome from Mytilus edulis during a seasonal spawning event in deep and shallow water culture sites on the northeast coast of Newfoundland, Canada. Mar Genomics 2021; 60:100865. [PMID: 33933383 DOI: 10.1016/j.margen.2021.100865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/23/2021] [Accepted: 03/15/2021] [Indexed: 11/29/2022]
Abstract
The blue mussel (Mytilus edulis) has global commercial and ecological importance both in wild and cultured conditions. However there is a qualitative and quantitative lack of knowledge of the molecular mechanisms associated with its reproductive physiology, especially with reference to environmental interactions. Here we initiated a transcriptomic analysis (RNA-sequencing (RNA-seq)) of the mantle from both sexes sampled during a seasonal spawning event and from two culture depths (shallow-5 m; deep- 15 m). Mantle libraries were produced from 3 males and 3 females sampled from each of two shallow sites and two deep sites for a total of 12 replicate male and 12 replicate female libraries (24 total libraries). Overall a total of 2.3 billion raw 100 base reads with an average of 96.5 million reads/library were obtained and assembled into 296,118 transcripts with an average length of 568 bp. Overall, 315 transcripts from male libraries and 25 from female libraries were found to be upregulated in deep water as compared to shallow (edgeR adjusted p value ≤ 0.05). Conversely, 126 transcripts from male libraries and 135 from female libraries were found to be significantly downregulated at the same depth. Thirteen transcripts were selected for qPCR validation based on importance in reproduction, antimicrobial defense and metabolism. Of these, 9 RNA-seq identified transcripts were shown by qPCR to be differentially expressed between groups: 2 were upregulated in deep compared with shallow water (dhx38, mt-co1), 2 were upregulated for female compared with male mantle (pias2, mapkap1) and 6 genes (fndc3a, acbd3, klhl10, ccnb3, armc4, mt-co1) showed to be upregulated in males compared to females. The majority of qPCR studied transcripts were identified as involved in gamete development based on the UniProt database. This study further characterizes the importance of the mantle transcriptome during reproductive activities of M. edulis.
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Affiliation(s)
- Daria Gallardi
- Fisheries and Oceans Canada, 80 East White Hills Road, PO Box 5667, St. John's, NL A1C 5X1, Canada.
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Eloi Mercier
- Canadian Centre for Computational Genomics - Montreal Node, McGill University and Genome Quebec Innovation Center, 740 Dr. Penfield Avenue, Montréal, Québec H3A 0G1, Canada
| | - Terry Mills
- Norlantic Processors Limited, P.O. Box 381, Botwood, NL A0H 1E0, Canada
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics - Montreal Node, McGill University and Genome Quebec Innovation Center, 740 Dr. Penfield Avenue, Montréal, Québec H3A 0G1, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Harry M Murray
- Fisheries and Oceans Canada, 80 East White Hills Road, PO Box 5667, St. John's, NL A1C 5X1, Canada
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12
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Wang YY, Duan SH, Wang GL, Li JL. Integrated mRNA and miRNA expression profile analysis of female and male gonads in Hyriopsis cumingii. Sci Rep 2021; 11:665. [PMID: 33436779 PMCID: PMC7804246 DOI: 10.1038/s41598-020-80264-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Hyriopsis cumingii is an important species for freshwater pearl cultivation in China. In terms of pearl production, males have larger pearls and better glossiness than females, but there are few reports focusing on the sex of H. cumingii. In this study, six mRNA and six microRNA (miRNA) libraries were prepared from ovaries and testes. Additionally, 28,502 differentially expressed genes (DEGs) and 32 differentially expressed miRNAs (DEMs) were identified. Compared with testis, 14,360 mRNAs and 20 miRNAs were up-regulated in ovary, 14,142 mRNAs and 12 miRNAs were down-regulated. In DEGs, the known genes related to sex determinism and/or differentiation were also identified, such as DMRT1, SOX9, SF1 for males, FOXL2 for females, and other potentially significant candidate genes. Three sex-related pathways have also been identified, which are Wnt, Notch, and TGF-beta. In 32 DEMs, the three miRNAs (miR-9-5p, miR-92, miR-184) were paid more attention, they predicted 28 target genes, which may also be candidates for sex-related miRNAs and genes. Differential miRNAs target genes analysis reveals the pathway associated with oocyte meiosis and spermatogenesis. Overall, the findings of the study provide significant insights to enhance our understanding of sex differentiation and/or sex determination mechanisms for H. cumingii.
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Affiliation(s)
- Ya-Yu Wang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Sheng-Hua Duan
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Gui-Ling Wang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Jia-Le Li
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
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Choi MJ, Oh YD, Kim YR, Lim HK, Kim JM. Use of a gene encoding zona pellucida 4 as a female-specific marker for early stage sexual differentiation and size dimorphism in the pacific abalone Haliotis discus hannai. Anim Reprod Sci 2021; 225:106687. [PMID: 33454618 DOI: 10.1016/j.anireprosci.2021.106687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022]
Abstract
Growth rates of Pacific abalone Haliotis discus hannai are an important trait affecting the economic value in the abalone aquaculture industry. A reverse-transcription polymerase chain reaction (RT-PCR) analyses of tissues from H. discus hannai was conducted for sexually mature gonads to determine male- and female-specific target gene expression, including genes encoding zona pellucida domain 4 (zp4), sperm protein (sp) and lysin (lys), respectively. Sex-specific expression patterns of these gene expression, even in sexually immature abalone, indicate these genes can be used as sensitive and robust sex-specific molecular markers. The RT-PCR procedure was also performed to analyze tissues collected at various developmental stages (50-day intervals) beginning at fertilization to determine when sex differentiation and expression of sex-specific genes was initiated. Detection of zp4 transcript in tissues collected at 200 days post-fertilization (dpf) indicated egg-specific development starts at 150-200 dpf. To evaluate possible sex-specific differences in growth rate, there was conducting of a molecular marker-based sex identification of abalone from a population selected for rapid growth rate. In a group of large H. discus hannai, females were more prevalent than males. To assess the correlation between growth and sex, there was comparison of weights of 3-year-old Pacific abalone in specimens where there had been sex determinations by visual examination and molecular methods. The results indicated females weighed more (55.92 ± 9.38 g, n = 15) than males (43.64 ± 15.55 g, n = 6, P = 0.037), indicating females had a more rapid growth rate than males.
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Affiliation(s)
- Mi-Jin Choi
- Department of Fisheries Biology, PuKyong National University, Busan, 48513, Republic of Korea
| | - Young Dae Oh
- Department of Biomedicine, Health & Life Convergence Sciences, BK21, College of Pharmacy Mokpo National University, Muan-gun 58554, Republic of Korea
| | - Yeo Reum Kim
- Department of Fisheries Biology, PuKyong National University, Busan, 48513, Republic of Korea
| | - Han Kyu Lim
- Department of Biomedicine, Health & Life Convergence Sciences, BK21, College of Pharmacy Mokpo National University, Muan-gun 58554, Republic of Korea.
| | - Jong-Myoung Kim
- Department of Fisheries Biology, PuKyong National University, Busan, 48513, Republic of Korea.
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Koutsouveli V, Cárdenas P, Santodomingo N, Marina A, Morato E, Rapp HT, Riesgo A. The Molecular Machinery of Gametogenesis in Geodia Demosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals. Mol Biol Evol 2020; 37:3485-3506. [PMID: 32929503 PMCID: PMC7743902 DOI: 10.1093/molbev/msaa183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
All animals are capable of undergoing gametogenesis. The ability of forming haploid cells from diploid cells through meiosis and recombination appeared early in eukaryotes, whereas further gamete differentiation is mostly a metazoan signature. Morphologically, the gametogenic process presents many similarities across animal taxa, but little is known about its conservation at the molecular level. Porifera are the earliest divergent animals and therefore are an ideal phylum to understand evolution of the gametogenic toolkits. Although sponge gametogenesis is well known at the histological level, the molecular toolkits for gamete production are largely unknown. Our goal was to identify the genes and their expression levels which regulate oogenesis and spermatogenesis in five gonochoristic and oviparous species of the genus Geodia, using both RNAseq and proteomic analyses. In the early stages of both female and male gametogenesis, genes involved in germ cell fate and cell-renewal were upregulated. Then, molecular signals involved in retinoic acid pathway could trigger the meiotic processes. During later stages of oogenesis, female sponges expressed genes involved in cell growth, vitellogenesis, and extracellular matrix reassembly, which are conserved elements of oocyte maturation in Metazoa. Likewise, in spermatogenesis, genes regulating the whole meiotic cycle, chromatin compaction, and flagellum axoneme formation, that are common across Metazoa were overexpressed in the sponges. Finally, molecular signals possibly related to sperm capacitation were identified during late stages of spermatogenesis for the first time in Porifera. In conclusion, the activated molecular toolkit during gametogenesis in sponges was remarkably similar to that deployed during gametogenesis in vertebrates.
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Affiliation(s)
- Vasiliki Koutsouveli
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Nadiezhda Santodomingo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Anabel Marina
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Esperanza Morato
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Hans Tore Rapp
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
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15
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Kim MA, Kim TH, Lee S, Nam BH, Lee JS, Jang W, Sohn YC. Ovarian transcriptome profiles associated with sexual maturation in Pacific abalone (Haliotis discus hannai). Genes Genomics 2020; 42:1179-1188. [PMID: 32804357 DOI: 10.1007/s13258-020-00983-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND There is now abundant information on genes involved in molluscan oogenesis and their associations with ovarian development. However, few studies have investigated the ovarian transcriptome of Pacific abalone (Haliotis discus hannai). OBJECTIVE The objective of this study was to identify genes related to ovarian development and maturation in Pacific abalone utilizing RNA-sequencing (RNA-seq) and to verify the genes most relevant to different stages of maturation. METHODS RNA samples from the ovarian tissues of sexually immature and mature abalone were used to construct cDNA libraries, which were paired-end sequenced on an Illumina HiSeq 2500 platform. Reads from individual samples (unigenes) were aligned to reference transcriptome databases for identification of differentially expressed genes (DEGs) between immature and mature ovarian libraries. Reverse transcription-quantitative polymerase chain reaction was used to verify the RNA-seq data. RESULTS A total of 8779 unigenes were obtained from the ovaries of immature and mature abalone, with a total length of 3323,279 bp and an average length of 379 bp per gene. Gene ontology analysis assigned 5860 unigenes to biological processes, 855 to cellular components, and 1352 to molecular functions. Overall, 470 DEGs were identified, including 213 and 257 genes down-regulated and up-regulated in mature abalone, respectively. Among these, 13 relevant transcripts, including VTG1 and FZD7, were significantly highly expressed in the ovaries of mature abalone (p < 0.05, fold change > 2). CONCLUSION This H. discus hannai ovary transcriptome provides molecular targets to better understand ovarian development, oogenesis, and sexual maturation, and to enhance Pacific abalone production.
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Affiliation(s)
- Mi Ae Kim
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon, 25457, Republic of Korea.,The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung, Gangwon, 25457, Republic of Korea
| | - Tae Ha Kim
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon, 25457, Republic of Korea
| | - Sora Lee
- Department of Life Science, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Jung Sick Lee
- Department of Aqualife Medicine, Chonnam National University, Yeosu, 59626, Republic of Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon, 25457, Republic of Korea.
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16
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Cherif-Feildel M, Heude Berthelin C, Adeline B, Rivière G, Favrel P, Kellner K. Molecular evolution and functional characterisation of insulin related peptides in molluscs: Contributions of Crassostrea gigas genomic and transcriptomic-wide screening. Gen Comp Endocrinol 2019; 271:15-29. [PMID: 30389328 DOI: 10.1016/j.ygcen.2018.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022]
Abstract
Insulin Related Peptides (IRPs) belong to the insulin superfamily and possess a typical structure with two chains, B and A, linked by disulphide bonds. As the sequence conservation is usually low between members, IRPs are classified according to the number and position of their disulphide bonds. In molluscan species, the first IRPs identified, named Molluscan Insulin-related Peptides (MIPs), exhibit four disulphide bonds. The genomic and transcriptomic data screening in the Pacific oyster Crassostrea gigas (Mollusc, Bivalvia) allowed us to identify six IRP sequences belonging to three structural groups. Cg-MIP1 to 4 have the typical structure of MIPs with four disulphide bonds. Cg-ILP has three disulphide bonds like vertebrate Insulin-Like Peptides (ILPs). The last one, Cg-MILP7 has a significant homology with Drosophila ILP7 (DILP7) associated with two additional cysteines allowing the formation of a fourth disulphide bond. The phylogenetic analysis points out that ILPs may be the most ancestral form. Moreover, it appears that ILP7 orthologs are probably anterior to lophotrochozoa and ecdysozoa segregation. In order to investigate the diversity of physiological functions of the oyster IRPs, we combine in silico expression data, qPCR measurements and in situ hybridization. The Cg-ilp transcript, mainly detected in the digestive gland and in the gonadal area, is potentially involved in the control of digestion and gametogenesis. The expression of Cg-mip4 is mainly associated with the larval development. The Cg-mip transcript shared by the Cg-MIP1, 2 and 3, is mainly expressed in visceral ganglia but its expression was also observed in the gonads of mature males. This pattern suggested the key roles of IRPs in the control of sexual reproduction in molluscan species.
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Affiliation(s)
- Maëva Cherif-Feildel
- Normandy University, Caen, France; University of Caen Normandie, Unity Biology of Organisms and Aquatic Ecosystems (BOREA), MNHN, Sorbonne University, UCN, CNRS, IRD, Esplanade de la Paix, 14032 Caen, France
| | - Clothilde Heude Berthelin
- Normandy University, Caen, France; University of Caen Normandie, Unity Biology of Organisms and Aquatic Ecosystems (BOREA), MNHN, Sorbonne University, UCN, CNRS, IRD, Esplanade de la Paix, 14032 Caen, France
| | - Beatrice Adeline
- Normandy University, Caen, France; University of Caen Normandie, Unity Biology of Organisms and Aquatic Ecosystems (BOREA), MNHN, Sorbonne University, UCN, CNRS, IRD, Esplanade de la Paix, 14032 Caen, France
| | - Guillaume Rivière
- Normandy University, Caen, France; University of Caen Normandie, Unity Biology of Organisms and Aquatic Ecosystems (BOREA), MNHN, Sorbonne University, UCN, CNRS, IRD, Esplanade de la Paix, 14032 Caen, France
| | - Pascal Favrel
- Normandy University, Caen, France; University of Caen Normandie, Unity Biology of Organisms and Aquatic Ecosystems (BOREA), MNHN, Sorbonne University, UCN, CNRS, IRD, Esplanade de la Paix, 14032 Caen, France
| | - Kristell Kellner
- Normandy University, Caen, France; University of Caen Normandie, Unity Biology of Organisms and Aquatic Ecosystems (BOREA), MNHN, Sorbonne University, UCN, CNRS, IRD, Esplanade de la Paix, 14032 Caen, France.
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17
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Johnson KM, Wong JM, Hoshijima U, Sugano CS, Hofmann GE. Seasonal transcriptomes of the Antarctic pteropod, Limacina helicina antarctica. MARINE ENVIRONMENTAL RESEARCH 2019; 143:49-59. [PMID: 30448238 DOI: 10.1016/j.marenvres.2018.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
High latitude seas will be among the first marine systems to be impacted by ocean acidification (OA). Previous research studying the effects of OA on the pteropod, Limacina helicina antarctica, has led this species to be identified as a sentinel organism for OA in polar oceans. Here, we present gene expression data on L. h. antarctica, collected in situ during the seasonal transition from early spring to early summer. Our findings suggest that after over-wintering under seasonal sea ice, pteropods progress toward full maturity in the early summer when food becomes increasingly available. This progression is highlighted by a dramatic shift in gene expression that supports the development of cytoskeletal structures, membrane ion transportation, and metabolically important enzymes associated with glycolysis. In addition, we observed signs of defense of genomic integrity and maturation as evidenced by an up-regulation of genes involved in DNA replication, DNA repair, and gametogenesis. These data contribute to a broader understanding of the life-cycle dynamics for L. h. antarctica and provide key insights into the transcriptomic signals of pteropod maturation and growth during this key seasonal transition.
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Affiliation(s)
- Kevin M Johnson
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Juliet M Wong
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Umihiko Hoshijima
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Cailan S Sugano
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA; Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
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18
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Tapia-Morales S, López-Landavery EA, Giffard-Mena I, Ramírez-Álvarez N, Gómez-Reyes RJE, Díaz F, Galindo-Sánchez CE. Transcriptomic response of the Crassostrea virginica gonad after exposure to a water-accommodation fraction of hydrocarbons and the potential implications in reproduction. Mar Genomics 2018; 43:9-18. [PMID: 30409725 DOI: 10.1016/j.margen.2018.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/06/2018] [Accepted: 10/20/2018] [Indexed: 11/26/2022]
Abstract
The Crassostrea virginica oyster has biological and economic importance in the Gulf of Mexico, an area with a high extraction and production of hydrocarbons. Exposure to hydrocarbons affects the reproductive processes in bivalves. In C. virginica, the effect of hydrocarbons on the gonad of the undifferentiated organism has not been evaluated to determine the possible damage during the maturation process. To evaluate this effect, RNA-seq data was generated from C. virginica gonads exposed to a 200 μg/L of hydrocarbons at different exposure times (7, 14 and 21 days) and a control treatment (without hydrocarbons). The analysis of the gonad transcriptome showed the negative effect of hydrocarbons on maturation, with a sub-expression of 22 genes involved in different stages of this process. Additionally, genes in the immune system were down-regulated, which may indicate that exposure to hydrocarbons causes immunosuppression in bivalves. A group of oxidative stress genes was also reduced. These data contribute to a better understanding of the effect of hydrocarbons on the reproductive process in bivalves and, at the same time, allow us to identify possible biomarkers associated with hydrocarbon contamination in the gonad of C. virginica.
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Affiliation(s)
- S Tapia-Morales
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico; Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Laboratorio de Patología Experimental Acuícola, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - E A López-Landavery
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - I Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Laboratorio de Patología Experimental Acuícola, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - N Ramírez-Álvarez
- Universidad Autónoma de Baja California, Instituto de Investigaciones Oceanológicas, Carretera Ensenada-Tijuana No. 3917, C.P. 22860 Ensenada, B. C., Mexico
| | - R J E Gómez-Reyes
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - F Díaz
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico
| | - C E Galindo-Sánchez
- Centro de Investigación Científica y Educación Superior de Ensenada, Laboratorio de Genómica Marina, Carretera Ensenada-Tijuana, C.P. 22860 Ensenada, B. C., Mexico.
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19
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Cherif-Feildel M, Kellner K, Goux D, Elie N, Adeline B, Lelong C, Heude Berthelin C. Morphological and molecular criteria allow the identification of putative germ stem cells in a lophotrochozoan, the Pacific oyster Crassostrea gigas. Histochem Cell Biol 2018; 151:419-433. [PMID: 30318560 DOI: 10.1007/s00418-018-1740-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2018] [Indexed: 11/30/2022]
Abstract
While our knowledge of bivalve gametogenesis recently progressed, data on early stages of gametogenesis remain to be developed, especially when dealing with germinal stem cells (GSC) and their niche in these organisms. Here, we wish to develop a strategy to identify putative GSC in Pacific oyster Crassostrea gigas based on morphological criteria combined with vasa marker expression. A histological quantitative approach, based on stereology, allowed us to identify two types of early germ cells in the germinal epithelium, one presenting round nuclei and the other irregular ones. Both early germ cell types present slightly condensed chromatin in nucleus, are vasa-positive and the Oyvlg (oyster vasa-like gene) expression in these cells is recorded throughout the whole gametogenesis process. The microenvironment of an early germ cell in oyster includes an associated somatic cell presenting an immunolabeling for BMP2/4 and a close myoid cell. In agreement with the GSC characteristics in other species, we postulate that putative germ stem cells in C. gigas correspond to the early germ cell type with irregular nucleus shape; those early germ cells with a round nucleus may consist in progenitors.
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Affiliation(s)
- Maëva Cherif-Feildel
- Normandy University, Caen, France.,Université de Caen Normandie, Unité mixte de recherche Biologie des Organismes et Ecosystèmes Aquatiques MNHN, Sorbonne Université, UCN, CNRS-7208, IRD-207, UA, Caen, France
| | - Kristell Kellner
- Normandy University, Caen, France.,Université de Caen Normandie, Unité mixte de recherche Biologie des Organismes et Ecosystèmes Aquatiques MNHN, Sorbonne Université, UCN, CNRS-7208, IRD-207, UA, Caen, France
| | - Didier Goux
- Normandy University, Caen, France.,Université de Caen Normandie, UNICAEN, SF 4206 ICORE, CMABIO3, 14000, Caen, France
| | - Nicolas Elie
- Normandy University, Caen, France.,Université de Caen Normandie, UNICAEN, SF 4206 ICORE, CMABIO3, 14000, Caen, France
| | - Béatrice Adeline
- Normandy University, Caen, France.,Université de Caen Normandie, Unité mixte de recherche Biologie des Organismes et Ecosystèmes Aquatiques MNHN, Sorbonne Université, UCN, CNRS-7208, IRD-207, UA, Caen, France
| | - Christophe Lelong
- Normandy University, Caen, France.,Université de Caen Normandie, Unité mixte de recherche Biologie des Organismes et Ecosystèmes Aquatiques MNHN, Sorbonne Université, UCN, CNRS-7208, IRD-207, UA, Caen, France
| | - Clothilde Heude Berthelin
- Normandy University, Caen, France. .,Université de Caen Normandie, Unité mixte de recherche Biologie des Organismes et Ecosystèmes Aquatiques MNHN, Sorbonne Université, UCN, CNRS-7208, IRD-207, UA, Caen, France.
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20
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Shi Y, Liu W, He M. Proteome and Transcriptome Analysis of Ovary, Intersex Gonads, and Testis Reveals Potential Key Sex Reversal/Differentiation Genes and Mechanism in Scallop Chlamys nobilis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:220-245. [PMID: 29546597 DOI: 10.1007/s10126-018-9800-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Bivalve mollusks exhibit hermaphroditism and sex reversal/differentiation. Studies generally focus on transcriptional profiling and specific genes related to sex determination and differentiation. Few studies on sex reversal/differentiation have been reported. A combination analysis of gonad proteomics and transcriptomics was conducted on Chlamys nobilis to provide a systematic understanding of sex reversal/differentiation in bivalves. We obtained 4258 unique peptides and 93,731 unigenes with good correlation between messenger RNA and protein levels. Candidate genes in sex reversal/differentiation were found: 15 genes differentially expressed between sexes were identified and 12 had obvious sexual functions. Three novel genes (foxl2, β-catenin, and sry) were expressed highly in intersex individuals and were likely involved in the control of gonadal sex in C. nobilis. High expression of foxl2 or β-catenin may inhibit sry and activate 5-HT receptor and vitellogenin to maintain female development. High expression of sry may inhibit foxl2 and β-catenin and activate dmrt2, fem-1, sfp2, sa6, Amy-1, APCP4, and PLK to maintain male function. High expression of sry, foxl2, and β-catenin in C. nobilis may be involved in promoting and maintaining sex reversal/differentiation. The downstream regulator may not be dimorphic expressed genes, but genes expressed in intersex individuals, males and females. Different expression patterns of sex-related genes and gonadal histological characteristics suggested that C. nobilis may change its sex from male to female. These findings suggest highly conserved sex reversal/differentiation with diverged regulatory pathways during C. nobilis evolution. This study provides valuable genetic resources for understanding sex reversal/differentiation (intersex) mechanisms and pathways underlying bivalve reproductive regulation.
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Affiliation(s)
- Yu Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Wenguang Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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21
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Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB. Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation. J Proteome Res 2017; 16:3298-3309. [PMID: 28730805 DOI: 10.1021/acs.jproteome.7b00288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico, to Alaska. These long-lived clams are highly fecund, although sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. The development of assays of gonad physiology could indicate sex and maturation stage as well as be used to assess the status of natural populations. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data-dependent acquisition (DDA) of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data were used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides that can be used as an efficient assay to determine geoduck gonad maturation status. Application of SRM in hemolymph samples demonstrates that this procedure could effectively be used to assess reproductive status in marine mollusks in a nonlethal manner.
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Affiliation(s)
- Emma B Timmins-Schiffman
- Department of Genome Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Grace A Crandall
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Brent Vadopalas
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Michael E Riffle
- Department of Biochemistry, University of Washington , Seattle, Washington 98105, United States
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington , Seattle, Washington 98105, United States
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington 98105, United States
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22
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Song S, Yu H, Li Q. Genome survey and characterization of reproduction-related genes in the Pacific oyster. INVERTEBR REPROD DEV 2017. [DOI: 10.1080/07924259.2017.1287780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shanshan Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
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23
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24
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Pannetier M, Chassot AA, Chaboissier MC, Pailhoux E. Involvement of FOXL2 and RSPO1 in Ovarian Determination, Development, and Maintenance in Mammals. Sex Dev 2016; 10:167-184. [PMID: 27649556 DOI: 10.1159/000448667] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Indexed: 11/19/2022] Open
Abstract
In mammals, sex determination is a process through which the gonad is committed to differentiate into a testis or an ovary. This process relies on a delicate balance between genetic pathways that promote one fate and inhibit the other. Once the gonad is committed to the female pathway, ovarian differentiation begins and, depending on the species, is completed during gestation or shortly after birth. During this step, granulosa cell precursors, steroidogenic cells, and primordial germ cells start to express female-specific markers in a sex-dimorphic manner. The germ cells then arrest at prophase I of meiosis and, together with somatic cells, assemble into functional structures. This organization gives the ovary its definitive morphology and functionality during folliculogenesis. Until now, 2 main genetic cascades have been shown to be involved in female sex differentiation. The first is driven by FOXL2, a transcription factor that also plays a crucial role in folliculogenesis and ovarian fate maintenance in adults. The other operates through the WNT/CTNNB1 canonical pathway and is regulated primarily by R-spondin1. Here, we discuss the roles of FOXL2 and RSPO1/WNT/ CTNNB1 during ovarian development and homeostasis in different models, such as humans, goats, and rodents.
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Affiliation(s)
- Maëlle Pannetier
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France
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25
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Transcriptome analysis of male and female mature gonads of Japanese scallop Patinopecten yessonsis. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0449-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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Mendoza-Porras O, Botwright NA, Reverter A, Cook MT, Harris JO, Wijffels G, Colgrave ML. Identification of differentially expressed reproductive and metabolic proteins in the female abalone (Haliotis laevigata) gonad following artificial induction of spawning. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 24:127-138. [PMID: 27268288 DOI: 10.1016/j.cbd.2016.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 04/14/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
Abstract
Inefficient control of temperate abalone spawning prevents pair-wise breeding and production of abalone with highly marketable traits. Traditionally, abalone farmers have used a combination of UV irradiation and application of temperature gradients to the tank water to artificially induce spawning. Proteins are known to regulate crucial processes such as respiration, muscle contraction, feeding, growth and reproduction. Spawning as a pre-requisite of abalone reproduction is likely to be regulated, in part, by endogenous proteins. A first step in elucidating the mechanisms that regulate spawning is to identify which proteins are directly involved during spawning. The present study examined protein expression following traditional spawning induction in the Haliotis laevigata female. Gonads were collected from abalone in the following physiological states: (1) spawning; (2) post-spawning; and (3) failed-to-spawn. Differential protein abundance was initially assessed using two-dimensional difference in-gel electrophoresis coupled with mass spectrometry for protein identification. A number of reproductive proteins such as vitellogenin, vitelline envelope zona pellucida domain 29 and prohibitin, and metabolic proteins such as thioredoxin peroxidase, superoxide dismutase and heat shock proteins were identified. Differences in protein abundance levels between physiological states were further assessed using scheduled multiple reaction monitoring mass spectrometry. Positive associations were observed between the abundance of specific proteins, such as heat shock cognate 70 and peroxiredoxin 6, and the propensity or failure to spawn in abalone. These findings have contributed to better understand both the effects of oxidative and heat stress over abalone physiology and their influence on abalone spawning.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia; School of Biological Sciences, Flinders University, GPO Box 2100, South Australia 5001, Australia; Australian Seafood Cooperative Research Centre, Science Park Adelaide, Laffer Drive, Bedford Park, South Australia 5042, Australia.
| | - Natasha A Botwright
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia.
| | - Antonio Reverter
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia.
| | - Mathew T Cook
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia.
| | - James O Harris
- School of Biological Sciences, Flinders University, GPO Box 2100, South Australia 5001, Australia.
| | - Gene Wijffels
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia.
| | - Michelle L Colgrave
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia.
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27
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Akcha F, Barranger A, Bachère E, Berthelin CH, Piquemal D, Alonso P, Sallan RR, Dimastrogiovanni G, Porte C, Menard D, Szczybelski A, Benabdelmouna A, Auffret M, Rouxel J, Burgeot T. Effects of an environmentally relevant concentration of diuron on oyster genitors during gametogenesis: responses of early molecular and cellular markers and physiological impacts. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8008-8020. [PMID: 26780042 DOI: 10.1007/s11356-015-5969-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
Genitors of the Pacific oyster Crassostrea gigas were submitted during gametogenesis to a short pulse exposure to the herbicide diuron at a realistic environmental concentration. Histological analysis showed no effect of diuron on gametogenesis course, sex ratio and reproductive effort. A non-significant increase in testosterone and progesterone levels was observed in genitors exposed to the herbicide. At cell level, diuron exposure was shown to modulate the phagocytic activity of circulating hemocytes. The results of a transcriptional analysis showed that diuron affected the expression of genes belonging to functions known to play a major role during oyster gametogenesis such as gene transcription regulation, DNA replication and repair, DNA methylation and cytokinesis. Taking into account the results we previously obtained on the same genitors, this study showed a negative effect of diuron on oyster reproduction by inducing both structural and functional modifications of the DNA.
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Affiliation(s)
- F Akcha
- Laboratoire d'Ecotoxicologie, Ifremer, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes cedex 03, France.
| | - A Barranger
- Laboratoire d'Ecotoxicologie, Ifremer, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes cedex 03, France
| | - E Bachère
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095, Montpellier, France
| | - C Heude Berthelin
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208), Université de Caen Normandie, Sorbonne Universités, Muséum national d'Histoire naturelle, Université Pierre et Marie Curie, CNRS, IRD, 57 rue Cuvier, 75005, Paris, France
| | - D Piquemal
- Acobiom, 1682 rue de la Valsière, CS 77394 Cap Delta Biopole Euromédecine II, 34184, Montpellier Cedex 04, France
| | - P Alonso
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095, Montpellier, France
| | - R Rondon Sallan
- Ifremer, UMR 5244, IHPE Interaction Host Pathogen Environment, UPVD, CNRS, Université de Montpellier, CC 80, F-34095, Montpellier, France
| | - G Dimastrogiovanni
- IDAEA-CSIC, Environmental Chemistry Department, C/ Jordi Girona, 1808034, Barcelona, Spain
| | - C Porte
- IDAEA-CSIC, Environmental Chemistry Department, C/ Jordi Girona, 1808034, Barcelona, Spain
| | - D Menard
- Laboratoire d'Ecotoxicologie, Ifremer, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes cedex 03, France
| | - A Szczybelski
- Laboratoire d'Ecotoxicologie, Ifremer, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes cedex 03, France
| | - A Benabdelmouna
- Ifremer, Laboratoire de Génétique et Pathologies, Rue de Mus de Loup, La Tremblade, 17390, France
| | - M Auffret
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer (IUEM), UBO/CNRS/IRD/IFREMER, rue Dumont d'Urville, technopôle, Brest-Iroise, 29280, Plouzané, France
| | - J Rouxel
- Laboratoire d'Ecotoxicologie, Ifremer, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes cedex 03, France
| | - T Burgeot
- Laboratoire d'Ecotoxicologie, Ifremer, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes cedex 03, France
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28
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GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. BMC Bioinformatics 2015; 16:401. [PMID: 26627443 PMCID: PMC4667447 DOI: 10.1186/s12859-015-0833-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 11/24/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. DESCRIPTION We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. CONCLUSIONS The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.
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29
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Sussarellu R, Huvet A, Lapègue S, Quillen V, Lelong C, Cornette F, Jensen LF, Bierne N, Boudry P. Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas. BMC Genomics 2015; 16:808. [PMID: 26483072 PMCID: PMC4613751 DOI: 10.1186/s12864-015-1972-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/03/2015] [Indexed: 02/07/2023] Open
Abstract
Background Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably recently in Northern Europe. Methods To explore potential adaptation of reproductive traits in populations with different histories, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Sex ratio, condition index and microarray gene expression in gonads, were analyzed in each progeny (n = 60). Results A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several transcripts differentially expressed between the Danish and French progenies, for which additive genetic basis is suspected (showing intermediate expression levels in hybrids, and therefore additivity). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism, known to be implicated in coordinated control and success of reproduction. Conclusions Observed differences suggest that adaptation of invasive populations might have occurred during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, gamete quality and fertility. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1972-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rossana Sussarellu
- Ifremer, Laboratoire des Sciences de l'Environnement Marin UMR 6539 (UBO/CNRS/IRD/Ifremer), Plouzané, France. .,Present address: Ifremer, Laboratoire d'Ecotoxicologie, Nantes, France.
| | - Arnaud Huvet
- Ifremer, Laboratoire des Sciences de l'Environnement Marin UMR 6539 (UBO/CNRS/IRD/Ifremer), Plouzané, France.
| | - Sylvie Lapègue
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390, La Tremblade, France.
| | - Virgile Quillen
- Ifremer, Laboratoire des Sciences de l'Environnement Marin UMR 6539 (UBO/CNRS/IRD/Ifremer), Plouzané, France.
| | - Christophe Lelong
- UNICAEN, UMR BOREA MNHN, UPMC, UNICAEN, CNRS-7208, IRD207, F-14032, Caen, France.
| | - Florence Cornette
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390, La Tremblade, France.
| | | | - Nicolas Bierne
- Université Montpellier 2, Montpellier, France. .,CNRS - Institut des Sciences de l'Evolution, UMR5554, Station Méditerranéenne de l'Environnement Littoral, Sète, France.
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l'Environnement Marin UMR 6539 (UBO/CNRS/IRD/Ifremer), Plouzané, France.
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Rivera-Perez C. Marine invertebrate lipases: Comparative and functional genomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 15:39-48. [PMID: 26114431 DOI: 10.1016/j.cbd.2015.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/20/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
Lipases are key enzymes involved in lipid digestion, storage and mobilization of reserves during fasting or heightened metabolic demand. This is a highly conserved process, essential for survival. The genomes of five marine invertebrate species with distinctive digestive system were screened for the six major lipase families. The two most common families in marine invertebrates, the neutral an acid lipases, are also the main families in mammals and insects. The number of lipases varies two-fold across analyzed genomes. A high degree of orthology with mammalian lipases was observed. Interestingly, 19% of the marine invertebrate lipases have lost motifs required for catalysis. Analysis of the lid and loop regions of the neutral lipases suggests that many marine invertebrates have a functional triacylglycerol hydrolytic activity as well as some acid lipases. A revision of the expression profiles and functional activity on sequences in databases and scientific literature provided information regarding the function of these families of enzymes in marine invertebrates.
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Affiliation(s)
- Crisalejandra Rivera-Perez
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA; Centro de Investigaciones Biologicas del Noroeste (CIBNOR), La Paz, B.C.S. 23096, Mexico.
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31
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Zhang Y, Mu H, Lau SCK, Zhang Z, Qiu JW. Sperm proteome of Mytilus galloprovincialis: Insights into the evolution of fertilization proteins in marine mussels. Proteomics 2015; 15:4175-9. [PMID: 26046548 DOI: 10.1002/pmic.201500066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/15/2015] [Accepted: 06/02/2015] [Indexed: 12/19/2022]
Abstract
Cataloging the sperm proteome of an animal can improve our understanding of its sperm-egg interaction and speciation, but such data are available for only a few free-spawning invertebrates. This study aimed to identify the sperm proteome of Mytilus galloprovincialis, a free-spawning marine mussel. We integrated public transcriptome datasets by de novo assembly, and applied SDS-PAGE coupled LC-MS/MS analysis to profile the sperm proteome, resulting in the identification of 550 proteins. Comparing the homologous sperm protein coding genes between M. galloprovincialis and its closely related species M. edulis revealed that fertilization proteins have the highest mean nonsynonymous substitution rate (Ka/Ks = 0.62) among 11 functional groups, consistent with previous reports of positive selection of several fertilization proteins in Mytilus. Moreover, 78 sperm proteins in different functional groups have Ka/Ks values > 0.5, indicating the presence of many candidate sperm proteins for further analysis of rapid interspecific divergence. The MS data are available in ProteomeXchange with the identifier PXD001665.
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Affiliation(s)
- Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
| | - Stanley C K Lau
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, P. R. China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China
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Teaniniuraitemoana V, Huvet A, Levy P, Gaertner-Mazouni N, Gueguen Y, Le Moullac G. Molecular signatures discriminating the male and the female sexual pathways in the pearl oyster Pinctada margaritifera. PLoS One 2015; 10:e0122819. [PMID: 25815473 PMCID: PMC4376701 DOI: 10.1371/journal.pone.0122819] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/24/2015] [Indexed: 11/30/2022] Open
Abstract
The genomics of economically important marine bivalves is studied to provide better understanding of the molecular mechanisms underlying their different reproductive strategies. The recently available gonad transcriptome of the black-lip pearl oyster Pinctada margaritifera is a novel and powerful resource to study these mechanisms in marine mollusks displaying hermaphroditic features. In this study, RNAseq quantification data of the P. margaritifera gonad transcriptome were analyzed to identify candidate genes in histologically-characterized gonad samples to provide molecular signatures of the female and male sexual pathway in this pearl oyster. Based on the RNAseq data set, stringent expression analysis identified 1,937 contigs that were differentially expressed between the gonad histological categories. From the hierarchical clustering analysis, a new reproduction model is proposed, based on a dual histo-molecular analytical approach. Nine candidate genes were identified as markers of the sexual pathway: 7 for the female pathway and 2 for the male one. Their mRNA levels were assayed by real-time PCR on a new set of gonadic samples. A clustering method revealed four principal expression patterns based on the relative gene expression ratio. A multivariate regression tree realized on these new samples and validated on the previously analyzed RNAseq samples showed that the sexual pathway of P. margaritifera can be predicted by a 3-gene-pair expression ratio model of 4 different genes: pmarg-43476, pmarg-foxl2, pmarg-54338 and pmarg-fem1-like. This 3-gene-pair expression ratio model strongly suggests only the implication of pmarg-foxl2 and pmarg-fem1-like in the sex inversion of P. margaritifera. This work provides the first histo-molecular model of P. margaritifera reproduction and a gene expression signature of its sexual pathway discriminating the male and female pathways. These represent useful tools for understanding and studying sex inversion, sex differentiation and sex determinism in this species and other related species for aquaculture purposes such as genetic selection programs.
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Affiliation(s)
- Vaihiti Teaniniuraitemoana
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre du Pacifique, BP 7004, 98719 Taravao, Tahiti, French Polynesia
| | - Arnaud Huvet
- Ifremer, UMR 6539 Laboratoire des sciences de l’Environnement Marin (LEMAR), ZI de la Pointe du Diable, CS 10070, F-29280 Plouzané, France
| | - Peva Levy
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre du Pacifique, BP 7004, 98719 Taravao, Tahiti, French Polynesia
| | - Nabila Gaertner-Mazouni
- Université de la Polynésie Française, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, BP 6570, 98702 Faa'a, Tahiti, French Polynesia
| | - Yannick Gueguen
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre du Pacifique, BP 7004, 98719 Taravao, Tahiti, French Polynesia
- Ifremer, UMR 5119 Ecologie des Systèmes Marins Côtiers (ECOSYM), Labex Corail, Université de Montpellier, Place Eugène Bataillon, CC 80, F-34095 Montpellier Cedex 5, France
| | - Gilles Le Moullac
- Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre du Pacifique, BP 7004, 98719 Taravao, Tahiti, French Polynesia
- * E-mail:
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Pauletto M, Milan M, de Sousa JT, Huvet A, Joaquim S, Matias D, Leitão A, Patarnello T, Bargelloni L. Insights into molecular features of Venerupis decussata oocytes: a microarray-based study. PLoS One 2014; 9:e113925. [PMID: 25470487 PMCID: PMC4254928 DOI: 10.1371/journal.pone.0113925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/31/2014] [Indexed: 11/18/2022] Open
Abstract
The production of Venerupis decussata relies on wild seed collection, which has been recently compromised due to recruitment failure and severe mortalities. To address this issue and provide an alternative source of seed, artificial spawning and larval rearing programs were developed. However, hatchery-based seed production is a relatively new industry and it is still underdeveloped. A major hurdle in the European clam seed production is the control of spawning and reproduction, which is further hindered by the impossibility of obtaining fertile gametes by gonadal "stripping", as meiosis re-initiation is constrained to a maturation process along the genital ducts. In the present study, oocytes were collected from 15 females and microarray analyses was performed to investigate gene expression profiles characterizing released and stripped ovarian oocytes. A total of 198 differentially expressed transcripts between stripped and spawned oocytes were detected. Functional analysis carried out on these transcripts highlighted the importance of a few biological processes, which are most probably implicated in the control of oocyte competence. Significant differences were observed for transcripts encoding proteins involved in meiosis progression (e.g. dual specificity phosphatase CDC25), WNT signalling (e.g. frizzled class receptor 8, wingless-type MMTV integration site family member 4), steroid synthesis (e.g. progestin and adipoQ receptor family member 3, cytochrome P450-C17), mRNA processing (e.g. zinc finger protein XlCOF28), calcium regulation (e.g. regucalcin, calmodulin) and ceramide metabolism (ceramidase B, sphingomyelinase). This study provides new information on transcriptional profiles putatively associated with ovarian egg infertility, and suggests potential mechanisms regulating early oocyte development in clams. Genes which were differentially expressed between stripped and spawned oocytes might have a pivotal role during maturation process in the gonadal duct and could be interesting targets for further functional studies aiming to make ovarian oocytes fertilizable.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
- * E-mail:
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Joana Teixeira de Sousa
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Laboratoire des Sciences de l’Environnement Marin, Plouzané, France
- IPMA, Instituto Português do Mar e da Atmosfera, Olhão, Portugal
| | - Arnaud Huvet
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Laboratoire des Sciences de l’Environnement Marin, Plouzané, France
| | - Sandra Joaquim
- IPMA, Instituto Português do Mar e da Atmosfera, Olhão, Portugal
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Domitília Matias
- IPMA, Instituto Português do Mar e da Atmosfera, Olhão, Portugal
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Alexandra Leitão
- IPMA, Instituto Português do Mar e da Atmosfera, Olhão, Portugal
- Environmental Studies Center, Qatar University, Doha, Qatar
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
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Cross I, Merlo MA, Rodríguez ME, Portela-Bens S, Rebordinos L. Adaptation to abiotic stress in the oyster Crassostrea angulata relays on genetic polymorphisms. FISH & SHELLFISH IMMUNOLOGY 2014; 41:618-624. [PMID: 25462456 DOI: 10.1016/j.fsi.2014.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
Here we describe the whole genome re-sequencing of the Portuguese oyster Crassostrea angulata, an edible cupped oyster of major commercial importance with an important role as biosensor of coastal water pollution. We sequenced the genome of the C. angulata to 29.3-fold coverage using ABI SOLID system. Comparisons of the sequences with the reference assembly of the Pacific oyster (Crassostrea gigas), yielded 129 million SNPs, 151,620 from which were located in 20,908 genes from the C. gigas database. The analysis of Gene Ontology (GO) terms associated with gene regions containing SNPs, revealed that significant GO terms showing differences between the two oyster species, were related to activities of response to stress caused both by drying and by metal contamination. In the Biological Process domain, the GO terms ion transport, phosphorylation and proteolysis processes, among others, showed many polymorphic genes in C. angulata. These processes are related to combating genotoxic and hypo-osmotic stress in the oyster. It is noteworthy that more than 200 polymorphic genes were associated with DNA repair processes. These results reveal that most of the gene polymorphisms observed in C. angulata are associated with processes related to genome adaptation to abiotic stress in estuarine regions and support that genetic polymorphisms may be the base to the observed ability of C. angulata to retain the phenomenally high concentrations of toxic heavy metals. Our results also provide the framework for future investigations to establish the molecular basis of phenotypic variation of adaptive traits and should contribute to the management of the species' genetic resources.
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Affiliation(s)
- Ismael Cross
- Laboratory of Genetics, Faculty of Marine and Environmental Sciences, CACYTMAR, University of Cadiz, Campus Río San Pedro, 11510 Puerto Real, Cadiz, Spain.
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Transcriptomic profiling of gametogenesis in triploid Pacific Oysters Crassostrea gigas: towards an understanding of partial sterility associated with triploidy. PLoS One 2014; 9:e112094. [PMID: 25375782 PMCID: PMC4222980 DOI: 10.1371/journal.pone.0112094] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/13/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Triploidy can occur in many animal species but is often lethal. Among invertebrates, amphibians and fishes, triploids are viable although often sterile or infertile. Most triploids of the Pacific oyster Crassostrea gigas are almost sterile (named "3nβ") yet a low but significant proportion show an advanced gametogenesis (named "3nα"). These oysters thus constitute an interesting model to study the effect of triploidy on germ cell development. We used microarrays to compare the gonad transcriptomes of diploid 2n and the abovementioned triploid 3nβ and 3nα male and female oysters throughout gametogenesis. RESULTS All triploids displayed an upregulation of genes related to DNA repair and apoptosis and a downregulation of genes associated with cell division. The comparison of 3nα and 3nβ transcriptomes with 2n revealed the likely involvement of a cell cycle checkpoint during mitosis in the successful but delayed development of gonads in 3nα individuals. In contrast, a disruption of sex differentiation mechanisms may explain the sterility of 3nβ individuals with 3nβ females expressing male-specific genes and 3nβ males expressing female-specific genes. CONCLUSIONS The disruption of sex differentiation and mitosis may be responsible for the impaired gametogenesis of triploid Pacific oysters. The function of the numerous candidate genes identified in our study should now be studied in detail in order to elucidate their role in sex determination, mitosis/meiosis control, pachytene cell cycle checkpoint, and the control of DNA repair/apoptosis.
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Genomic analysis of the Pacific oyster (Crassostrea gigas) reveals possible conservation of vertebrate sex determination in a mollusc. G3-GENES GENOMES GENETICS 2014; 4:2207-17. [PMID: 25213692 PMCID: PMC4232546 DOI: 10.1534/g3.114.013904] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Despite the prevalence of sex in animal kingdom, we have only limited understanding of how sex is determined and evolved in many taxa. The mollusc Pacific oyster Crassostrea gigas exhibits complex modes of sexual reproduction that consists of protandric dioecy, sex change, and occasional hermaphroditism. This complex system is controlled by both environmental and genetic factors through unknown molecular mechanisms. In this study, we investigated genes related to sex-determining pathways in C. gigas through transcriptome sequencing and analysis of female and male gonads. Our analysis identified or confirmed novel homologs in the oyster of key sex-determining genes (SoxH or Sry-like and FoxL2) that were thought to be vertebrate-specific. Their expression profile in C. gigas is consistent with conserved roles in sex determination, under a proposed model where a novel testis-determining CgSoxH may serve as a primary regulator, directly or indirectly interacting with a testis-promoting CgDsx and an ovary-promoting CgFoxL2. Our findings plus previous results suggest that key vertebrate sex-determining genes such as Sry and FoxL2 may not be inventions of vertebrates. The presence of such genes in a mollusc with expression profiles consistent with expected roles in sex determination suggest that sex determination may be deeply conserved in animals, despite rapid evolution of the regulatory pathways that in C. gigas may involve both genetic and environmental factors.
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Exploiting genomic data to identify proteins involved in abalone reproduction. J Proteomics 2014; 108:337-53. [DOI: 10.1016/j.jprot.2014.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/31/2023]
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Teaniniuraitemoana V, Huvet A, Levy P, Klopp C, Lhuillier E, Gaertner-Mazouni N, Gueguen Y, Le Moullac G. Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes. BMC Genomics 2014; 15:491. [PMID: 24942841 PMCID: PMC4082630 DOI: 10.1186/1471-2164-15-491] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Black pearl farming is based on culture of the blacklip pearl oyster Pinctada margaritifera (Mollusca, lophotrochozoa), a protandrous hermaphrodite species. At first maturation, all individuals are males. The female sex appears progressively from two years old, which represents a limitation for broodstock conditioning for aquaculture production. In marine mollusks displaying hermaphroditic features, data on sexual determinism and differentiation, including the molecular sex determining cascade, are scarce. To increase genomic resources and identify the molecular mechanisms whereby gene expression may act in the sexual dimorphism of P. margaritifera, we performed gonad transcriptome analysis. RESULTS The gonad transcriptome of P. margaritifera was sequenced from several gonadic samples of males and females at different development stages, using a Next-Generation-Sequencing method and RNAseq technology. After Illumina sequencing, assembly and annotation, we obtained 70,147 contigs of which 62.2% shared homologies with existing protein sequences, and 9% showed functional annotation with Gene Ontology terms. Differential expression analysis identified 1,993 differentially expressed contigs between the different categories of gonads. Clustering methods of samples revealed that the sex explained most of the variation in gonad gene expression. K-means clustering of differentially expressed contigs showed 815 and 574 contigs were more expressed in male and female gonads, respectively. The analysis of these contigs revealed the presence of known specific genes coding for proteins involved in sex determinism and/or differentiation, such as dmrt and fem-1 like for males, or foxl2 and vitellogenin for females. The specific gene expression profiles of pmarg-fem1-like, pmarg-dmrt and pmarg-foxl2 in different reproductive stages (undetermined, sexual inversion and regression) suggest that these three genes are potentially involved in the sperm-oocyte switch in P. margaritifera. CONCLUSIONS The study provides a new transcriptomic tool to study reproduction in hermaphroditic marine mollusks. It identifies sex differentiation and potential sex determining genes in P. margaritifera, a protandrous hermaphrodite species.
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Affiliation(s)
| | | | | | | | | | | | | | - Gilles Le Moullac
- Ifremer, UMR 241 EIO, Labex CORAIL, BP 7004, 98719 Taravao, Tahiti, Polynésie Française.
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Olson CE, Roberts SB. Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes. Front Physiol 2014; 5:224. [PMID: 24987376 PMCID: PMC4060414 DOI: 10.3389/fphys.2014.00224] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 01/21/2023] Open
Abstract
DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity.
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Affiliation(s)
- Claire E Olson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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de Sousa JT, Milan M, Bargelloni L, Pauletto M, Matias D, Joaquim S, Matias AM, Quillien V, Leitão A, Huvet A. A microarray-based analysis of gametogenesis in two Portuguese populations of the European clam Ruditapes decussatus. PLoS One 2014; 9:e92202. [PMID: 24643002 PMCID: PMC3958495 DOI: 10.1371/journal.pone.0092202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/19/2014] [Indexed: 02/01/2023] Open
Abstract
The European clam, Ruditapes decussatus is a species with a high commercial importance in Portugal and other Southern European countries. Its production is almost exclusively based on natural recruitment, which is subject to high annual fluctuations. Increased knowledge of the natural reproductive cycle of R. decussatus and its molecular mechanisms would be particularly important in providing new highly valuable genomic information for better understanding the regulation of reproduction in this economically important aquaculture species. In this study, the transcriptomic bases of R. decussatus reproduction have been analysed using a custom oligonucleotide microarray representing 51,678 assembled contigs. Microarray analyses were performed in four gonadal maturation stages from two different Portuguese wild populations, characterized by different responses to spawning induction when used as progenitors in hatchery. A comparison between the two populations elucidated a specific pathway involved in the recognition signals and binding between the oocyte and components of the sperm plasma membrane. We suggest that this pathway can explain part of the differences in terms of spawning induction success between the two populations. In addition, sexes and reproductive stages were compared and a correlation between mRNA levels and gonadal area was investigated. The lists of differentially expressed genes revealed that sex explains most of the variance in gonadal gene expression. Additionally, genes like Foxl2, vitellogenin, condensing 2, mitotic apparatus protein p62, Cep57, sperm associated antigens 6, 16 and 17, motile sperm domain containing protein 2, sperm surface protein Sp17, sperm flagellar proteins 1 and 2 and dpy-30, were identified as being correlated with the gonad area and therefore supposedly with the number and/or the size of the gametes produced.
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Affiliation(s)
- Joana Teixeira de Sousa
- IFREMER, UMR CNRS 6539, Laboratoire des Sciences de l'Environnement Marin, Plouzané, France
- IPMA, Olhão, Portugal
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Legnaro, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Legnaro, Italy
| | | | | | | | - Virgile Quillien
- IFREMER, UMR CNRS 6539, Laboratoire des Sciences de l'Environnement Marin, Plouzané, France
| | | | - Arnaud Huvet
- IFREMER, UMR CNRS 6539, Laboratoire des Sciences de l'Environnement Marin, Plouzané, France
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Matsumoto T, Masaoka T, Fujiwara A, Nakamura Y, Satoh N, Awaji M. Reproduction-related genes in the pearl oyster genome. Zoolog Sci 2013; 30:826-50. [PMID: 24125647 DOI: 10.2108/zsj.30.826] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molluscan reproduction has been a target of biological research because of the various reproductive strategies that have evolved in this phylum. It has also been studied for the development of fisheries technologies, particularly aquaculture. Although fundamental processes of reproduction in other phyla, such as vertebrates and arthropods, have been well studied, information on the molecular mechanisms of molluscan reproduction remains limited. The recently released draft genome of the pearl oyster Pinctada fucata provides a novel and powerful platform for obtaining structural information on the genes and proteins involved in bivalve reproduction. In the present study, we analyzed the pearl oyster draft genome to screen reproduction-related genes. Analysis was mainly conducted for genes reported from other molluscs for encoding orthologs of reproduction-related proteins in other phyla. The gene search in the P. fucata gene models (version 1.1) and genome assembly (version 1.0) were performed using Genome Browser and BLAST software. The obtained gene models were then BLASTP searched against a public database to confirm the best-hit sequences. As a result, more than 40 gene models were identified with high accuracy to encode reproduction-related genes reported for P. fucata and other molluscs. These include vasa, nanos, doublesex- and mab-3-related transcription factor, 5-hydroxytryptamine (5-HT) receptors, vitellogenin, estrogen receptor, and others. The set of reproduction-related genes of P. fucata identified in the present study constitute a new tool for research on bivalve reproduction at the molecular level.
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Affiliation(s)
- Toshie Matsumoto
- 1 Aquaculture Technology Division, National Research Institute of Aquaculture, Fisheries Research Agency, Minami-lse, Watarai, Mie 516-0193, Japan
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Guévélou E, Huvet A, Galindo-Sánchez CE, Milan M, Quillien V, Daniel JY, Quéré C, Boudry P, Corporeau C. Sex-Specific Regulation of AMP-Activated Protein Kinase (AMPK) in the Pacific Oyster Crassostrea gigas1. Biol Reprod 2013; 89:100. [DOI: 10.1095/biolreprod.113.109728] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Jouaux A, Lafont M, Blin JL, Houssin M, Mathieu M, Lelong C. Physiological change under OsHV-1 contamination in Pacific oyster Crassostrea gigas through massive mortality events on fields. BMC Genomics 2013; 14:590. [PMID: 23987141 PMCID: PMC3766697 DOI: 10.1186/1471-2164-14-590] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Massive mortalities have been observed in France since 2008 on spat and juvenile Pacific oysters, Crassostrea gigas. A herpes virus called OsHV-1, easily detectable by PCR, has been implicated in the mortalities as demonstrated by the results of numerous field studies linking mortality with OsHV-1 prevalence. Moreover, experimental infections using viral particles have documented the pathogenicity of OsHV-1 but the physiological responses of host to pathogen are not well known. RESULTS The aim of this study was to understand mechanisms brought into play against the virus during infection in the field. A microarray assay has been developed for a major part of the oyster genome and used for studying the host transcriptome across mortality on field. Spat with and without detectable OsHV-1 infection presenting or not mortality respectively were compared by microarray during mortality episodes. In this study, a number of genes are regulated in the response to pathogen infection on field and seems to argue to an implication of the virus in the observed mortality. The result allowed establishment of a hypothetic scheme of the host cell's infection by, and response to, the pathogen. CONCLUSIONS This response shows a "sensu stricto" innate immunity through genic regulation of the virus OsHV-1 life cycle, but also others biological processes resulting to complex interactions between host and pathogens in general.
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Affiliation(s)
- Aude Jouaux
- CNRS INEE, BioMEA, Caen Cedex 14 032, France
- Biologie des Organismes Marins et des Ecosystèmes Associés (BioMEA), IBFA, SFR ICORE, Université de Caen Basse-Normandie, Caen Cedex 14032, France
- Centre de Référence sur l’Huître, Université de Caen Basse Normandie, Caen Cedex 14 032, France
| | - Maxime Lafont
- CNRS INEE, BioMEA, Caen Cedex 14 032, France
- Biologie des Organismes Marins et des Ecosystèmes Associés (BioMEA), IBFA, SFR ICORE, Université de Caen Basse-Normandie, Caen Cedex 14032, France
- Centre de Référence sur l’Huître, Université de Caen Basse Normandie, Caen Cedex 14 032, France
| | - Jean-Louis Blin
- Centre de Référence sur l’Huître, Université de Caen Basse Normandie, Caen Cedex 14 032, France
- Synergie Mer Et Littoral, Zone conchylicole, Blainville sur mer 50 560, France
| | - Maryline Houssin
- Centre de Référence sur l’Huître, Université de Caen Basse Normandie, Caen Cedex 14 032, France
- Laboratoire Frank Duncombe, Saint Contest Cedex 4 14 053, France
| | - Michel Mathieu
- CNRS INEE, BioMEA, Caen Cedex 14 032, France
- Biologie des Organismes Marins et des Ecosystèmes Associés (BioMEA), IBFA, SFR ICORE, Université de Caen Basse-Normandie, Caen Cedex 14032, France
- Centre de Référence sur l’Huître, Université de Caen Basse Normandie, Caen Cedex 14 032, France
| | - Christophe Lelong
- CNRS INEE, BioMEA, Caen Cedex 14 032, France
- Biologie des Organismes Marins et des Ecosystèmes Associés (BioMEA), IBFA, SFR ICORE, Université de Caen Basse-Normandie, Caen Cedex 14032, France
- Centre de Référence sur l’Huître, Université de Caen Basse Normandie, Caen Cedex 14 032, France
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