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Le Franc L, Petton B, Favrel P, Rivière G. m 6A Profile Dynamics Indicates Regulation of Oyster Development by m 6A-RNA Epitranscriptomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:742-755. [PMID: 36496129 PMCID: PMC10787124 DOI: 10.1016/j.gpb.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.
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Affiliation(s)
- Lorane Le Franc
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Bruno Petton
- Ifremer, Laboratoire des Sciences de l'Environnement Marin, UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne, 29280 Plouzané, France
| | - Pascal Favrel
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Guillaume Rivière
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France.
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Haque MA, Hossain MT, Islam MS, Islam MZ, Islam P, Shaha SN, Sikder MH, Rafiq K. Isolation of multidrug-resistant Escherichia coli and Salmonella spp. from sulfonamide-treated diarrheic calves. Vet World 2022; 15:2870-2876. [PMID: 36718340 PMCID: PMC9880849 DOI: 10.14202/vetworld.2022.2870-2876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Background and Aim The bovine industry is threatened by one of the most serious and deadly enteric diseases, calf diarrhea, particularly in developing nations like Bangladesh. In this context, bacterial resistance to antimicrobial drugs and its detrimental consequences have become a critical public health issue that is difficult to address globally. This study aimed to isolate and identify Escherichia coli and Salmonella spp. with their antibiogram and antibiotic resistance gene detection from sulfonamide-treated diarrheic calves. Materials and Methods Twelve diarrheic calves suffering from calf diarrhea in a dairy farm were selected and a total of 36 fecal samples were aseptically collected directly from rectum before, during, and at the end of treatment for each calf to determine the total viable count, total E. coli count and total Salmonella count. A polymerase chain reaction was used for the specific detection of E. coli and Salmonella genus targeting fliC and invA genes, respectively. Antibiotic sensitivity test of the isolated E. coli and Salmonella spp. were performed by the disk diffusion method for eight commonly used antibiotics. Results A total of 36 E. coli (100%) and 12 Salmonella spp. (33%) were isolated from the samples and were confirmed by polymerase chain reaction. Total viable count was found to be ranged from 35 × 107 to 99 × 1010 colony-forming unit (CFU)/g fecal sample before starting sulfonamide treatment, 34 × 105 to 25 × 1010 CFU/g during treatment with sulfonamide, and 48 × 103 to 69 × 1010 CFU/g immediately after completion of sulfonamide treatment. Total E. coli count was found to be ranged from 4 × 104 to 36 × 1010 CFU/g, 24 × 104 to 23 × 108 CFU/g, and 13 × 104 to 85 × 1010 CFU/g, whereas total Salmonella count was found to be ranged from 16 × 106 to 18.5 × 1011 CFU/g, 15 × 104 to 44 × 107 CFU/g, and 13.2 × 105 to 21 × 1010 CFU/g fecal sample before starting sulfonamide treatment, during treatment with sulfonamide immediately after completion of sulfonamide treatment, respectively. The in vitro antibiotic sensitivity test showed that all the E. coli and Salmonella spp. isolated from diarrheic calves (100%) contained multidrug-resistant (MDR) phenotypes. Escherichia coli isolates were found 100% resistant to amoxicillin (AMX), cefuroxime, cephalexin (CN), erythromycin (ERY), and tetracycline (TET); whereas 94.4%, 86.1%, and 77.8% isolates were resistant to doxycycline (DOX), moxifloxacin (MOF), and gentamycin (GEN), respectively. In case of Salmonella isolates, all were found 100% resistant to AMX, CN, and ERY; whereas 91.7% of resistance was observed for DOX, MOF, cefuroxime, GEN, and TET. Based on the molecular screening of the antibiotic resistance genes, tetA gene was present in 83.3% of the isolated E. coli and 75% of the isolated Salmonella strains, whereas 83.3% E. coli and 79.2% Salmonella isolates contained blaTEM gene. Conclusion These findings suggest that MDR E. coli and Salmonella spp. might be responsible for calf scouring, which is challenging to treat with antibiotics or sulfonamide drugs alone. Therefore, it is important to check the antibiotic sensitivity pattern to select a suitable antibiotic for the treatment of calf scoring. A suitable antibiotic or combination of an antibiotic and sulfonamide could be effective against E. coli and Salmonella spp. responsible for calf scouring.
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Affiliation(s)
| | | | - Md. Shafiqul Islam
- Department of Pharmacology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Zahorul Islam
- Department of Pharmacology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Purba Islam
- Department of Pharmacology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Mahmudul Hasan Sikder
- Department of Pharmacology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Kazi Rafiq
- Department of Pharmacology, Bangladesh Agricultural University, Mymensingh, Bangladesh,Corresponding author: Kazi Rafiq, e-mail: Co-authors: MAH: , MTH: , MSI: , MZI: , PI: , SNS: , MHS:
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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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Fernández-González LE, Sánchez-Marín P, Gestal C, Beiras R, Diz AP. Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105315. [PMID: 33853012 DOI: 10.1016/j.marenvres.2021.105315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Vitellogenin (Vtg), a large multidomain protein precursor of egg-yolk proteins, is used as an endocrine disruption biomarker in fish, and in the last decades, its use has been extended to invertebrates like mollusks. However, it remains unclear whether invertebrate endocrine system produces Vtg in response to estrogens, like it occurs in oviparous vertebrates. In a previous study, no evidence of induction of Vtg expression at protein level was found in gonads of the marine mussel Mytilus galloprovincialis after exposure to the estrogenic chemical 17α-ethinylestradiol (EE2). In the present follow-up study, it was investigated whether there is any effect of EE2 on Vtg abundance at transcriptional level in M. galloprovincialis gonads. To this aim, RT-qPCR analysis targeting three different domains of Vtg transcript was performed on gonads of mussels that were exposed either 4 or 24 days to 100 ng/L EE2. In addition, several reference genes were analysed and a selection of these for potential use in further RT-qPCR analyses on mussel male and female gonads is provided. Results showed higher expression in females than in males for the three analysed Vtg domains, and no evidence of Vtg mRNA induction due to EE2 either in females or males. The present results, together with those obtained from previous analysis at protein level, support that Vtg is not an adequate biomarker for xenoestrogenicity in marine mussels. Additionally, nucleotide sequences of Vtg transcripts of three closely-related species from Mytilus edulis complex (M. galloprovincialis, M. edulis and M. trossulus) are provided and compared with Vtg sequences from other mollusk species to assess the level of conservation and evolutionary relationships among species.
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Affiliation(s)
- Laura Emilia Fernández-González
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Paula Sánchez-Marín
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, 36390, Vigo, Spain
| | - Camino Gestal
- Marine Molecular Pathobiology Group, Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Ricardo Beiras
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Angel P Diz
- Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.
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Dou M, Jiao YH, Zheng JW, Zhang G, Li HY, Liu JS, Yang WD. De novo transcriptome analysis of the mussel Perna viridis after exposure to the toxic dinoflagellate Prorocentrum lima. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110265. [PMID: 32045784 DOI: 10.1016/j.ecoenv.2020.110265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Diarrheic shellfish poisoning (DSP) toxins are produced by harmful microalgae and accumulate in bivalve mollusks, causing various toxicity. These toxic effects appear to abate with increasing DSP concentration and longer exposure time, however, the underlying mechanisms remain unclear. To explore the underlying molecular mechanisms, de novo transcriptome analysis of the digestive gland of Perna viridis was performed after Prorocentrum lima exposure. RNA-seq analysis showed that 1886 and 237 genes were up- and down-regulated, respectively after 6 h exposure to P. lima, while 265 genes were up-regulated and 217 genes were down-regulated after 96 h compared to the control. These differentially expressed genes mainly involved in Nrf2 signing pathways, immune stress, apoptosis and cytoskeleton, etc. Combined with qPCR results, we speculated that the mussel P. viridis might mainly rely on glutathione S-transferase (GST) and ABC transporters to counteract DSP toxins during short-term exposure. However, longer exposure of P. lima could activate the Nrf2 signaling pathway and inhibitors of apoptosis protein (IAP), which in turn reduced the damage of DSP toxins to the mussel. DSP toxins could induce cytoskeleton destabilization and had some negative impact on the immune system of bivalves. Collectively, our findings uncovered the crucial molecular mechanisms and the regulatory metabolic nodes that underpin the defense mechanism of bivalves against DSP toxins and also advanced our current understanding of bivalve defense mechanisms.
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Affiliation(s)
- Min Dou
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China.
| | - Yu-Hu Jiao
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Jian-Wei Zheng
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hong-Ye Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Jie-Sheng Liu
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Wei-Dong Yang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China.
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Proestou DA, Sullivan ME. Variation in global transcriptomic response to Perkinsus marinus infection among eastern oyster families highlights potential mechanisms of disease resistance. FISH & SHELLFISH IMMUNOLOGY 2020; 96:141-151. [PMID: 31809834 DOI: 10.1016/j.fsi.2019.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Dermo disease, caused by the protozoan parasite Perkinsus marinus, negatively impacts wild and cultured Eastern oyster populations, yet our knowledge of the mechanistic bases for parasite pathogenicity and the Eastern oyster's response to it is limited. To better understand host responses to the parasite and identify molecular mechanisms underlying disease-resistance phenotypes, we experimentally challenged two families exhibiting divergent Dermo-resistance phenotypes with the parasite, generated global expression profiles using RNAseq and identified differentially expressed transcripts between control and challenged oysters from each family at multiple time points post-parasite injection. The susceptible and resistant families exhibited strikingly different transcriptomic responses to the parasite over a 28-day time period. The resistant family exhibited a strong, focused, early response to P. marinus infection, where many significantly upregulated transcripts were associated with the biological processes "regulation of proteolysis" and "oxidation-reduction process." P. marinus virulence factors are mainly comprised of proteases that facilitate parasite invasion and weaken host humoral defenses, thus host upregulation of transcripts associated with negative regulation of proteolysis is consistent with a Dermo-resistant phenotype. In contrast, the susceptible family mounted a very weak, disorganized, initial response to the parasite. Few transcripts were differentially expressed between control and injected oysters, and no functional enrichment was detected among them. At the final 28 d time point 2450 differentially expressed transcripts were identified and were associated with either "G-protein coupled receptor activity" (upregulated) or "microtubule-based process" (downregulated). A handful of protease inhibitors were differentially expressed between control and injected susceptible oysters, but this function was not enriched in the susceptible data set. The differential expression patterns observed in this study provide valuable insight into the functional basis of Dermo resistance and suggest that the timing of expression is just as important as the transcripts being expressed.
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Affiliation(s)
- Dina A Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
| | - Mary E Sullivan
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA; University of Rhode Island, Department of Fisheries, Animal and Veterinary Science, 460 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
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Zhao L, Li Y, Lou J, Yang Z, Liao H, Fu Q, Guo Z, Lian S, Hu X, Bao Z. Transcriptomic Profiling Provides Insights into Inbreeding Depression in Yesso Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:623-633. [PMID: 31300903 DOI: 10.1007/s10126-019-09907-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/30/2019] [Indexed: 06/10/2023]
Abstract
Inbreeding often causes a decline in biological fitness, known as inbreeding depression. In genetics study, inbreeding coefficient f gives the proportion by which the heterozygosity of an individual is reduced by inbreeding. With the development of high-throughput sequencing, researchers were able to perform deep approaches to investigate which genes are affected by inbreeding and reveal some molecular underpinnings of inbreeding depression. As one commercially important species, Yesso scallop Patinopecten yessoensis confront the same dilemma of inbreeding depression. To examine how inbreeding affects gene expression, we compared the transcriptome of two experimentally selfing families with inbreeding coefficient f reached 0.5 as well as one natural population (f ≈ 0) of P. yessoensis. A total of 24 RNA-Seq libraries were constructed using scallop adductor muscle, and eventually 676.56 M (96.85%) HQ reads were acquired. Based on differential gene analysis, we were able to identify nine common differentially expressed genes (DEGs) across the top-ranked 30 DEGs in both selfing families in comparation with the natural population. Remarkable, through weighted gene co-expression network analysis (WGCNA), five common DEGs were found enriched in the most significant inbreeding related functional module M14 (FDR = 1.64E-156), including SREBP1, G3BP2, SBK1, KIAA1161, and AATs-Glupro. These five genes showed significantly higher expression in self-bred progeny. Suggested by the genetic functional analysis, up-regulated SREBP1, G3BP2, and KIAA1161 may suggest a perturbing lipid metabolism, a severe inframammary reaction or immune response, and a stress-responsive behavior. Besides, the significant higher SBK1 and AATs-Glupro may reflect the abnormal cellular physiological situation. Together, these genetic aberrant transcriptomic performances may contribute to inbreeding depression in P. yessoensis, deteriorating the stress tolerance and survival phenotype in self-bred progeny. Our results would lay a foundation for further comprehensive understanding of bivalve inbreeding depression, which may potentially benefit the genetic breeding for scallop aquaculture.
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Affiliation(s)
- Liang Zhao
- Key Laboratory of Marine Genetics and Breeding (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
| | - Yangping Li
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Jiarun Lou
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Zhihui Yang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Huan Liao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Qiang Fu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Zhenyi Guo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Shanshan Lian
- Key Laboratory of Marine Genetics and Breeding (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.
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (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
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (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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Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas. Genes (Basel) 2019; 10:genes10090695. [PMID: 31509985 PMCID: PMC6771004 DOI: 10.3390/genes10090695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022] Open
Abstract
Histone methylation patterns are important epigenetic regulators of mammalian development, notably through stem cell identity maintenance by chromatin remodeling and transcriptional control of pluripotency genes. But, the implications of histone marks are poorly understood in distant groups outside vertebrates and ecdysozoan models. However, the development of the Pacific oyster Crassostrea gigas is under the strong epigenetic influence of DNA methylation, and Jumonji histone-demethylase orthologues are highly expressed during C. gigas early life. This suggests a physiological relevance of histone methylation regulation in oyster development, raising the question of functional conservation of this epigenetic pathway in lophotrochozoan. Quantification of histone methylation using fluorescent ELISAs during oyster early life indicated significant variations in monomethyl histone H3 lysine 4 (H3K4me), an overall decrease in H3K9 mono- and tri-methylations, and in H3K36 methylations, respectively, whereas no significant modification could be detected in H3K27 methylation. Early in vivo treatment with the JmjC-specific inhibitor Methylstat induced hypermethylation of all the examined histone H3 lysines and developmental alterations as revealed by scanning electronic microscopy. Using microarrays, we identified 376 genes that were differentially expressed under methylstat treatment, which expression patterns could discriminate between samples as indicated by principal component analysis. Furthermore, Gene Ontology revealed that these genes were related to processes potentially important for embryonic stages such as binding, cell differentiation and development. These results suggest an important physiological significance of histone methylation in the oyster embryonic and larval life, providing, to our knowledge, the first insights into epigenetic regulation by histone methylation in lophotrochozoan development.
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Li Y, Zhang L, Li R, Zhang M, Li Y, Wang H, Wang S, Bao Z. Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis. BMC Genomics 2019; 20:288. [PMID: 30975074 PMCID: PMC6460854 DOI: 10.1186/s12864-019-5661-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/31/2019] [Indexed: 12/15/2022] Open
Abstract
Background Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selection a vital step in RT-qPCR experiments. However, previous studies in mollusks only focused on the reference genes widely used in vertebrates. Results In this study, we conducted the transcriptome-wide identification of reference genes in the bivalve mollusk Mizuhopecten yessoensis based on 60 transcriptomes covering early development, adult tissues and gonadal development. A total of 964, 1210 and 2097 candidate reference genes were identified, respectively, resulting in a core set of 568 genes. Functional enrichment analysis showed that these genes are significantly overrepresented in Gene Ontology (GO) terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to ribosomes, energy production, etc. Six genes (RS23, EF1A, NDUS4, SELR1, EIF3F, and OLA1) were selected from the candidate genes for RT-qPCR validation, together with 6 commonly used reference genes (ACT, CYTC, HEL, EF1B, GAPDH and RPL16). Stability analyses using geNorm, NormFinder and the comparative delta-Ct method revealed that the new candidate reference genes are more stable than the traditionally used genes, and ACT and CYTC are not recommended under either of the three circumstances. There was a significant correlation between the Ct of RT-qPCR and the log2(TPM) of RNA-Seq data (Ct = − 0.94 log2(TPM) + 29.67, R2 = 0.73), making it easy to estimate the Ct values from transcriptome data prior to RT-qPCR experiments. Conclusion Our study represents the first transcriptome-wide identification of reference genes for early development, adult tissues, and gonadal development in the Yesso scallop and will benefit gene expression studies in other bivalve mollusks. Electronic supplementary material The online version of this article (10.1186/s12864-019-5661-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Meiwei Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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10
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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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11
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Briones C, Nuñez JJ, Pérez M, Espinoza-Rojas D, Molina-Quiroz C, Guiñez R. De novo male gonad transcriptome draft for the marine mussel Perumytilus purpuratus with a focus on its reproductive-related proteins. J Genomics 2018; 6:127-132. [PMID: 30510598 PMCID: PMC6275399 DOI: 10.7150/jgen.27864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/04/2018] [Indexed: 12/17/2022] Open
Abstract
Perumytilus purpuratus is a marine mussel considered a bioengineer species with a broad distribution in the Pacific and Atlantic coast of South America. Studies have shown two geographically and genetically differentiated subpopulations at molecular level and in sperm morphological traits. To open avenues for molecular research on P. purpuratus, a global de novo transcriptome from gonadal tissue of mature males was sequenced using the Illumina platform. From a total of 126.38 million reads, 37,765 transcripts were successfully annotated. BUSCO analysis determined a level of 89% completeness for the assembled transcriptome. The functional gene ontology (GO) annotation indicated that, in terms of abundance, the transcripts related with molecular function were the most represented, followed by those related with biological process and cellular components. Additionally, a subset of GO annotations generated using the "sperm" term resulted in a total of 1,294 sequences where the biological process category was the more represented, with transcripts strongly associated to sperm-processes required for fertilization, and with processes where the sperm-egg interaction could be implicated. Our work will contribute to the evolutionary understanding of the molecular mechanisms related to tissue-specific functions. This work reports the first male gonad transcriptome for the mussel P. purpuratus, generating a useful transcriptomic resource for this species and other closely related mytilids.
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Affiliation(s)
- Carolina Briones
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Montse Pérez
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36200 Vigo, España
| | | | | | - Ricardo Guiñez
- Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
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12
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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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13
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Xin L, Huang B, Bai C, Wang C. Validation of housekeeping genes for quantitative mRNA expression analysis in OsHV-1 infected ark clam, Scapharca broughtonii. J Invertebr Pathol 2018; 155:44-51. [DOI: 10.1016/j.jip.2018.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/24/2018] [Accepted: 04/30/2018] [Indexed: 01/21/2023]
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14
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fam20C participates in the shell formation in the pearl oyster, Pinctada fucata. Sci Rep 2018; 8:3563. [PMID: 29476076 PMCID: PMC5824888 DOI: 10.1038/s41598-018-21797-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/12/2018] [Indexed: 12/16/2022] Open
Abstract
Kinase-family with sequence similarity 20, member C (Fam20C) is a protein kinase, which can phosphorylate biomineralization related proteins in vertebrate animals. However, the function of Fam20C in invertebrate animals especially the role in biomineralization is still unknown. Herein, we cloned the cDNA of fam20C from the pearl oyster, Pinctada fucata. It is showed that the expression of fam20C in the mantle edge was much higher than other tissues. In situ hybridization showed that fam20C was expressed mostly in the outer epithelial cells of the middle fold, indicating it may play important roles in the shell formation. Besides, fam20C expression increased greatly in the D-shape stage of pearl oyster development, when the shell was first formed. During the shell repair process, the expression level of fam20C increased 1.5 times at 6 h after shell notching. Knockdown of fam20C in vivo by RNA interference resulted in abnormally stacking of calcium carbonate crystals at the edges of nacre tablets, showing direct evidence that fam20C participates in the shell formation. This study provides an insight into the role of kinase protein in the shell formation in mollusk and broaden our understanding of biomineralization mechanism.
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15
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Pazos AJ, Ventoso P, Martínez-Escauriaza R, Pérez-Parallé ML, Blanco J, Triviño JC, Sánchez JL. Transcriptional response after exposure to domoic acid-producing Pseudo-nitzschia in the digestive gland of the mussel Mytilus galloprovincialis. Toxicon 2017; 140:60-71. [PMID: 29031804 DOI: 10.1016/j.toxicon.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/28/2017] [Accepted: 10/08/2017] [Indexed: 01/19/2023]
Abstract
Bivalve molluscs are filter feeding species that can accumulate biotoxins in their body tissues during harmful algal blooms. Amnesic Shellfish Poisoning (ASP) is caused by species of the diatom genus Pseudo-nitzschia, which produces the toxin domoic acid. The Mytilus galloprovincialis digestive gland transcriptome was de novo assembled based on the sequencing of 12 cDNA libraries, six obtained from control mussels and six from mussels naturally exposed to domoic acid-producing diatom Pseudo-nitzschia australis. After de novo assembly 94,727 transcripts were obtained, with an average length of 1015 bp and a N50 length of 761 bp. The assembled transcripts were clustered (homology > 90%) into 69,294 unigenes. Differential gene expression analysis was performed (DESeq2 algorithm) in the digestive gland following exposure to the toxic algae. A total of 1158 differentially expressed unigenes (absolute fold change > 1.5 and p-value < 0.05) were detected: 686 up-regulated and 472 down-regulated. Several membrane transporters belonging to the family of the SLC (solute carriers) were over-expressed in exposed mussels. Functional enrichment was performed using Pfam annotations obtained from the genes differentially expressed, 37 Pfam families were found to be significantly (FDR adjusted p-value < 0.1) enriched. Some of these families (sulfotransferases, aldo/keto reductases, carboxylesterases, C1q domain and fibrinogen C-terminal globular domain) could be putatively involved in detoxification processes, in the response against of the oxidative stress and in immunological processes. Protein network analysis with STRING algorithm found alteration of the Notch signaling pathway under the action of domoic acid-producing Pseudo-nitzschia. In conclusion, this study provides a high quality reference transcriptome of M. galloprovincialis digestive gland and identifies potential genes involved in the response to domoic acid.
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Affiliation(s)
- Antonio J Pazos
- Departamento de Bioquímica y Biología Molecular, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
| | - Pablo Ventoso
- Departamento de Bioquímica y Biología Molecular, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Roi Martínez-Escauriaza
- Departamento de Bioquímica y Biología Molecular, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - M Luz Pérez-Parallé
- Departamento de Bioquímica y Biología Molecular, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Juan Blanco
- Centro de Investigacións Mariñas, Xunta de Galicia, Pedras de Corón s/n Apdo 13, Vilanova de Arousa, 36620, Spain
| | - Juan C Triviño
- Sistemas Genómicos, Ronda G. Marconi 6, Paterna, Valencia, 46980, Spain
| | - José L Sánchez
- Departamento de Bioquímica y Biología Molecular, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
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16
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Schultz JH, Adema CM. Comparative immunogenomics of molluscs. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:3-15. [PMID: 28322934 PMCID: PMC5494275 DOI: 10.1016/j.dci.2017.03.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/10/2017] [Accepted: 03/15/2017] [Indexed: 05/22/2023]
Abstract
Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity. Initial studies showed that the Mollusca (second largest animal phylum), and invertebrates in general, possess innate defenses but lack the lymphocytic immune system that characterizes vertebrate immunology. Recognizing the reality of both common and taxon-specific immune features, and applying up-to-date cell and molecular research capabilities, in-depth studies of a select number of bivalve and gastropod species continue to reveal novel aspects of molluscan immunity. The genomics era heralded a new stage of comparative immunology; large-scale efforts yielded an initial set of full molluscan genome sequences that is available for analyses of full complements of immune genes and regulatory sequences. Next-generation sequencing (NGS), due to lower cost and effort required, allows individual researchers to generate large sequence datasets for growing numbers of molluscs. RNAseq provides expression profiles that enable discovery of immune genes and genome sequences reveal distribution and diversity of immune factors across molluscan phylogeny. Although computational de novo sequence assembly will benefit from continued development and automated annotation may require some experimental validation, NGS is a powerful tool for comparative immunology, especially increasing coverage of the extensive molluscan diversity. To date, immunogenomics revealed new levels of complexity of molluscan defense by indicating sequence heterogeneity in individual snails and bivalves, and members of expanded immune gene families are expressed differentially to generate pathogen-specific defense responses.
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Affiliation(s)
- Jonathan H Schultz
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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17
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Song H, Dang X, He YQ, Zhang T, Wang HY. Selection of housekeeping genes as internal controls for quantitative RT-PCR analysis of the veined rapa whelk ( Rapana venosa). PeerJ 2017; 5:e3398. [PMID: 28584723 PMCID: PMC5455708 DOI: 10.7717/peerj.3398] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Background The veined rapa whelk Rapana venosa is an important commercial shellfish in China and quantitative real-time PCR (qRT-PCR) has become the standard method to study gene expression in R. venosa. For accurate and reliable gene expression results, qRT-PCR assays require housekeeping genes as internal controls, which display highly uniform expression in different tissues or stages of development. However, to date no studies have validated housekeeping genes in R. venosa for use as internal controls for qRT-PCR. Methods In this study, we selected the following 13 candidate genes for suitability as internal controls: elongation factor-1α (EF-1α), α-actin (ACT), cytochrome c oxidase subunit 1 (COX1), nicotinamide adenine dinucleotide dehydrogenase (ubiquinone) 1α subcomplex subunit 7 (NDUFA7), 60S ribosomal protein L5 (RL5), 60S ribosomal protein L28 (RL28), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β-tubulin (TUBB), 40S ribosomal protein S25 (RS25), 40S ribosomal protein S8 (RS8), ubiquitin-conjugating enzyme E2 (UBE2), histone H3 (HH3), and peptidyl-prolyl cis-trans isomerase A (PPIA). We measured the expression levels of these 13 candidate internal controls in eight different tissues and twelve larvae developmental stages by qRT-PCR. Further analysis of the expression stability of the tested genes was performed using GeNorm and RefFinder algorithms. Results Of the 13 candidate genes tested, we found that EF-1α was the most stable internal control gene in almost all adult tissue samples investigated with RL5 and RL28 as secondary choices. For the normalization of a single specific tissue, we suggested that EF-1α and NDUFA7 are the best combination in gonad, as well as COX1 and RL28 for intestine, EF-1α and RL5 for kidney, EF-1α and COX1 for gill, EF-1α and RL28 for Leiblein and mantle, EF-1α, RL5, and NDUFA7 for liver, GAPDH, PPIA, and RL28 for hemocyte. From a developmental perspective, we found that RL28 was the most stable gene in all developmental stages measured, and COX1 and RL5 were appropriate secondary choices. For the specific developmental stage, we recommended the following combination for normalization, PPIA, RS25, and RL28 for stage 1, RL5 and RL28 for stage 2 and 5, RL28 and NDUFA7 for stage 3, and PPIA and TUBB for stage 4. Discussion Our results are instrumental for the selection of appropriately validated housekeeping genes for use as internal controls for gene expression studies in adult tissues or larval development of R. venosa in the future.
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Affiliation(s)
- Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin Dang
- College of Fisheries, Ocean University of China, Qingdao, China
| | - Yuan-Qiu He
- College of Fisheries, Ocean University of China, Qingdao, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Yan Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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18
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Wang H, Zhang X, Liu Q, Liu X, Ding S. Selection and evaluation of new reference genes for RT-qPCR analysis in Epinephelus akaara based on transcriptome data. PLoS One 2017; 12:e0171646. [PMID: 28182746 PMCID: PMC5300273 DOI: 10.1371/journal.pone.0171646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 01/24/2017] [Indexed: 12/15/2022] Open
Abstract
Groupers are an economically important fish species in world fishery markets. Because many studies using RT-qPCR have addressed gene expression in groupers, appropriate reference genes are required to obtain reliable and accurate results. In this study, the most suitable reference genes were identified from eleven candidate genes of one of the most valuable species, Epinephelus akaara, in a range of different experimental conditions. Using the software packages geNorm, NormFinder, BestKeeper and refFinder, three traditionally used reference genes, β-actin (β-ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-2-microglobulin (B2M), were identified as not suitable for E. akaara gene expression studies, whereas two newly identified reference genes, conserved oligomeric Golgi complex subunit 5 (Cog5) and brefeldin a-inhibited guanine nucleotide-exchange protein 1 (ARFGEF1), could be universally applied under all the tested conditions. These data provide the foundation for more precise results in RT-qPCR studies of gene expression in E. akaara and other Epinephelus species.
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Affiliation(s)
- Huan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiang Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qiaohong Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- * E-mail:
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19
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Pardo BG, Álvarez-Dios JA, Cao A, Ramilo A, Gómez-Tato A, Planas JV, Villalba A, Martínez P. Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray. FISH & SHELLFISH IMMUNOLOGY 2016; 59:331-344. [PMID: 27815201 DOI: 10.1016/j.fsi.2016.10.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/17/2016] [Accepted: 10/30/2016] [Indexed: 06/06/2023]
Abstract
The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in response to B. ostreae through massively sequencing and has aided to improve our knowledge of the immune mechanisms of flat oyster. The validated oligo-microarray and the establishment of a reference transcriptome will be useful for large-scale gene expression studies in this species.
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Affiliation(s)
- Belén G Pardo
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidade de Santiago de Compostela, 15781 Santiago de Compostela, Spain.
| | - Asunción Cao
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
| | - Andrea Ramilo
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
| | - Antonio Gómez-Tato
- Departamento de Matemáticas, Facultad de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Josep V Planas
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08007, Barcelona, Spain.
| | - Antonio Villalba
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871 Alcalá de Henares, Spain.
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
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Huan P, Wang H, Liu B. Assessment of housekeeping genes as internal references in quantitative expression analysis during early development of oyster. Genes Genet Syst 2016; 91:257-265. [PMID: 27582049 DOI: 10.1266/ggs.16-00007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The early development of mollusks exhibits important characteristics from the developmental and evolutionary perspective. With the increasing number of genome-wide studies, accurate analyses of quantitative gene expression during development are impeded by the lack of validated reference genes. To improve the situation, in this study, we analyzed the expression stability of seven candidate housekeeping genes during early development of the Pacific oyster Crassostrea gigas: actin, glyceraldehyde-3-phosphate dehydrogenase (gapdh), α subunit of elongation factor 1 (elf1α), adp-ribosylation factor 1 (arf1), heterogeneous nuclear ribonucleoprotein q, ubiquitin-conjugating enzyme e2d2 and ribosomal protein s18. We focused on 11 stages from oocyte to D-veliger, which include crucial developmental processes such as axis determination, gastrulation and shell formation. Gene expression stabilities were assessed with the three commonly used programs geNorm, NormFinder and BestKeeper. Although the results obtained with the three programs varied to some extent, in general, arf1, elf1α and gapdh were highly ranked and actin was poorly ranked. This analysis also indicated that multiple genes should be used for normalization, and we concluded that arf1-elf1α-gapdh should be used as internal references. The findings of this study will help researchers to obtain accurate results in future quantitative gene expression analysis of development in bivalve mollusks.
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Affiliation(s)
- Pin Huan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
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Dineshram R, Chandramouli K, Ko GWK, Zhang H, Qian PY, Ravasi T, Thiyagarajan V. Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors. GLOBAL CHANGE BIOLOGY 2016; 22:2054-2068. [PMID: 26990129 DOI: 10.1111/gcb.13249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.
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Affiliation(s)
- Ramadoss Dineshram
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Kondethimmanahalli Chandramouli
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ginger Wai Kuen Ko
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Huoming Zhang
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Timothy Ravasi
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
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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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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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Huan P, Wang H, Liu B. A Label-Free Proteomic Analysis on Competent Larvae and Juveniles of the Pacific Oyster Crassostrea gigas. PLoS One 2015; 10:e0135008. [PMID: 26247880 PMCID: PMC4527670 DOI: 10.1371/journal.pone.0135008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/17/2015] [Indexed: 11/19/2022] Open
Abstract
Current understandings on the molecular mechanisms underlying bivalve metamorphosis are still fragmentary, and a comprehensive description is required. In this study, using a large-scale label-free proteomic approach, we described and compared the proteomes of competent larvae (CL) and juveniles (JU) of the Pacific oyster, Crassostrea gigas. A total of 788 proteins were identified: 392 in the CL proteome and 636 in the JU proteome. Gene Ontology analysis of the proteome from each sample revealed active metabolic processes in both stages. Further quantitative analyses revealed 117 proteins that were differentially expressed between the two samples. These proteins were divided into eight groups: cytoskeleton and cell adhesion, protein synthesis and degradation, immunity and stress response, development of particular tissues, signal regulation, metabolism and energy supply, transport, and other proteins. A certification experiment using real-time PCR assay confirmed 20 of 30 examined genes exhibited the same trends at the mRNA and protein levels. The differentially expressed proteins may play roles in tissue remodeling, signal transduction, and organ development during and after metamorphosis. Novel roles were proposed for some differentially expressed proteins, such as chymotrypsin. The results of this work provide an overview of metamorphosis and post-metamorphosis development of C. gigas at the protein level. Future studies on the functions of the differentially expressed proteins will help to obtain a more in-depth understanding of bivalve metamorphosis.
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Affiliation(s)
- Pin Huan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hongxia Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Baozhong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
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Dallas LJ, Jha AN. Applications of biological tools or biomarkers in aquatic biota: A case study of the Tamar estuary, South West England. MARINE POLLUTION BULLETIN 2015; 95:618-633. [PMID: 25817310 DOI: 10.1016/j.marpolbul.2015.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/15/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Biological systems are the ultimate recipients of pollutant-induced damage. Consequently, our traditional reliance on analytical tools is not enough to assess ecosystem health. Biological responses or biomarkers are therefore also considered to be important tools for environmental hazard and risk assessments. Due to historical mining, other anthropogenic activities, and its conservational importance (e.g. NATURA sites, SACs), the Tamar estuary in South West England is an ideal environment in which to examine applications of such biological tools. This review presents a thorough and critical evaluation of the different biological tools used in the Tamar estuary thus far, while also discussing future perspectives for biomarker studies from a global perspective. In particular, we focus on the challenges which hinder applications of biological tools from being more readily incorporated into regulatory frameworks, with the aim of enabling both policymakers and primary stakeholders to maximise the environmental relevance and regulatory usefulness of such tools.
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Affiliation(s)
- Lorna J Dallas
- School of Biological Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
| | - Awadhesh N Jha
- School of Biological Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK.
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26
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The use of -omic tools in the study of disease processes in marine bivalve mollusks. J Invertebr Pathol 2015; 131:137-54. [PMID: 26021714 DOI: 10.1016/j.jip.2015.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/09/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023]
Abstract
Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in the bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show that epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress -omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.
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Romero A, Forn-Cuní G, Moreira R, Milan M, Bargelloni L, Figueras A, Novoa B. An immune-enriched oligo-microarray analysis of gene expression in Manila clam (Venerupis philippinarum) haemocytes after a Perkinsus olseni challenge. FISH & SHELLFISH IMMUNOLOGY 2015; 43:275-286. [PMID: 25555813 DOI: 10.1016/j.fsi.2014.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/19/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
Parasites of the genus Perkinsus cause high mortality and economic losses in bivalves commonly produced in global aquaculture. Although the immune responses of oysters and clams naturally infected with Perkinsus marinus or Perkinsus olseni have been extensively studied, there is not much information on host response at the early stages of infection. In this study, we analysed how P. olseni influences the gene expression profiles of haemocytes from the Manila clam (Venerupis philippinarum) using temporal experimental infections and an immune-enriched microarray. We identified an early phase of infection that was characterised by no mortality and by the increased expression of genes associated with pathogen recognition, production of nitrogen radicals and antimicrobial activity. Cellular processes such as inhibition of serine proteases and proliferation were also involved in this early response. This phase was followed by an intermediate stage, when the pathogen was most likely multiplying and infecting new areas of the body, and animals began to die. In this stage, many genes related to cell movement were over-expressed. Thirty days after infection metabolic pathway genes were the most affected. Apoptosis appears to be important during pathogenesis. Our results provide novel observations of the broader innate immune response triggered by P. olseni at different infection stages.
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Affiliation(s)
- Alejandro Romero
- Institute of Marine Research, IIM - CSIC, Eduardo Cabello, 6, 362018 Vigo, Spain
| | - Gabriel Forn-Cuní
- Institute of Marine Research, IIM - CSIC, Eduardo Cabello, 6, 362018 Vigo, Spain
| | - Rebeca Moreira
- Institute of Marine Research, IIM - CSIC, Eduardo Cabello, 6, 362018 Vigo, Spain
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Antonio Figueras
- Institute of Marine Research, IIM - CSIC, Eduardo Cabello, 6, 362018 Vigo, Spain
| | - Beatriz Novoa
- Institute of Marine Research, IIM - CSIC, Eduardo Cabello, 6, 362018 Vigo, Spain.
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Temperature influences histone methylation and mRNA expression of the Jmj-C histone-demethylase orthologues during the early development of the oyster Crassostrea gigas. Mar Genomics 2015; 19:23-30. [DOI: 10.1016/j.margen.2014.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/08/2023]
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Dheilly NM, Duval D, Mouahid G, Emans R, Allienne JF, Galinier R, Genthon C, Dubois E, Du Pasquier L, Adema CM, Grunau C, Mitta G, Gourbal B. A family of variable immunoglobulin and lectin domain containing molecules in the snail Biomphalaria glabrata. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 48:234-43. [PMID: 25451302 PMCID: PMC4255472 DOI: 10.1016/j.dci.2014.10.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/17/2014] [Accepted: 10/18/2014] [Indexed: 05/04/2023]
Abstract
Technical limitations have hindered comprehensive studies of highly variable immune response molecules that are thought to have evolved due to pathogen-mediated selection such as fibrinogen-related proteins (FREPs) from Biomphalaria glabrata. FREPs combine upstream immunoglobulin superfamily (IgSF) domains with a C-terminal fibrinogen-related domain (FreD) and participate in reactions against trematode parasites. From RNAseq data we assembled a de novo reference transcriptome of B. glabrata to investigate the diversity of FREP transcripts. This study increased over two fold the number of bonafide FREP subfamilies and revealed important sequence diversity within FREP12 subfamily. We also report the discovery of related molecules that feature one or two IgSF domains associated with different C-terminal lectin domains, named C-type lectin-related proteins (CREPs) and Galectin-related protein (GREP). Together, the highly similar FREPs, CREPs and GREP were designated VIgL (Variable Immunoglobulin and Lectin domain containing molecules).
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Affiliation(s)
- Nolwenn M Dheilly
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France.
| | - David Duval
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Gabriel Mouahid
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Rémi Emans
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Jean-François Allienne
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Richard Galinier
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Clémence Genthon
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, Montpellier F-34396, France
| | - Emeric Dubois
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, Montpellier F-34396, France
| | - Louis Du Pasquier
- University of Basel, Institute of Zoology and Evolutionary Biology, Basel CH-4051, Switzerland
| | - Coen M Adema
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christoph Grunau
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Guillaume Mitta
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France
| | - Benjamin Gourbal
- CNRS, UMR 5244, Ecologie et Evolution des Interactions (2EI), Perpignan F-66860, France; Université de Perpignan Via Domitia, Perpignan F-66860, France.
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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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López-Landavery EA, Portillo-López A, Gallardo-Escárate C, Del Río-Portilla MA. Selection of reference genes as internal controls for gene expression in tissues of red abalone Haliotis rufescens (Mollusca, Vetigastropoda; Swainson, 1822). Gene 2014; 549:258-65. [PMID: 25101866 DOI: 10.1016/j.gene.2014.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/04/2014] [Accepted: 08/01/2014] [Indexed: 01/05/2023]
Abstract
The red abalone Haliotis rufescens is one of the most important species for aquaculture in Baja California, México, and despite this, few gene expression studies have been done in tissues such as gill, head and gonad. For this purpose, reverse transcription and quantitative real time PCR (RT-qPCR) is a powerful tool for gene expression evaluation. For a reliable analysis, however, it is necessary to select and validate housekeeping genes that allow proper transcription quantification. Stability of nine housekeeping genes (ACTB, BGLU, TUBB, CY, GAPDH, HPRTI, RPL5, SDHA and UBC) was evaluated in different tissues of red abalone (gill, head and gonad/digestive gland). Four-fold serial dilutions of cDNA (from 25 ngμL(-1) to 0.39 ngμL(-1)) were used to prepare the standard curve, and it showed gene efficiencies between 0.95 and 0.99, with R(2)=0.99. geNorm and NormFinder analysis showed that RPL5 and CY were the most stable genes considering all tissues, whereas in gill HPRTI and BGLU were most stable. In gonad/digestive gland, RPL5 and TUBB were the most stable genes with geNorm, while SDHA and HPRTI were the best using NormFinder. Similarly, in head the best genes were RPL5 and UBC with geNorm, and GAPDH and CY with NormFinder. The technical variability analysis with RPL5 and abalone gonad/digestive gland tissue indicated a high repeatability with a variation coefficient within groups ≤ 0.56% and between groups ≤ 1.89%. These results will help us for further research in reproduction, thermoregulation and endocrinology in red abalone.
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Affiliation(s)
- Edgar A López-Landavery
- Laboratorio de Genética, Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada N° 3918, Zona Playitas C.P 22860, Ensenada BC, Mexico
| | - Amelia Portillo-López
- Facultad de Ciencias, Universidad Autónoma de Baja California, Km 103 Carretera Tijuana-Ensenada, C.P 22860, Ensenada BC, Mexico
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile
| | - Miguel A Del Río-Portilla
- Laboratorio de Genética, Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada N° 3918, Zona Playitas C.P 22860, Ensenada BC, Mexico.
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Segarra A, Mauduit F, Faury N, Trancart S, Dégremont L, Tourbiez D, Haffner P, Barbosa-Solomieu V, Pépin JF, Travers MA, Renault T. Dual transcriptomics of virus-host interactions: comparing two Pacific oyster families presenting contrasted susceptibility to ostreid herpesvirus 1. BMC Genomics 2014; 15:580. [PMID: 25012085 PMCID: PMC4111845 DOI: 10.1186/1471-2164-15-580] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 07/01/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Massive mortality outbreaks affecting Pacific oyster (Crassostrea gigas) spat in various countries have been associated with the detection of a herpesvirus called ostreid herpesvirus type 1 (OsHV-1). However, few studies have been performed to understand and follow viral gene expression, as it has been done in vertebrate herpesviruses. In this work, experimental infection trials of C. gigas spat with OsHV-1 were conducted in order to test the susceptibility of several bi-parental oyster families to this virus and to analyze host-pathogen interactions using in vivo transcriptomic approaches. RESULTS The divergent response of these oyster families in terms of mortality confirmed that susceptibility to OsHV-1 infection has a significant genetic component. Two families with contrasted survival rates were selected. A total of 39 viral genes and five host genes were monitored by real-time PCR. Initial results provided information on (i) the virus cycle of OsHV-1 based on the kinetics of viral DNA replication and transcription and (ii) host defense mechanisms against the virus. CONCLUSIONS In the two selected families, the detected amounts of viral DNA and RNA were significantly different. This result suggests that Pacific oysters are genetically diverse in terms of their susceptibility to OsHV-1 infection. This contrasted susceptibility was associated with dissimilar host gene expression profiles. Moreover, the present study showed a positive correlation between viral DNA amounts and the level of expression of selected oyster genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Tristan Renault
- Ifremer (Institut Français de Recherche pour l'Exploitation de la Mer), Unité Santé Génétique et Microbiologie des Mollusques (SG2M), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Avenue de Mus de Loup, 17390 La Tremblade, France.
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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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Moreira R, Milan M, Balseiro P, Romero A, Babbucci M, Figueras A, Bargelloni L, Novoa B. Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray. BMC Genomics 2014; 15:267. [PMID: 24708293 PMCID: PMC4234419 DOI: 10.1186/1471-2164-15-267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 03/31/2014] [Indexed: 01/11/2023] Open
Abstract
Background The Manila clam (Ruditapes philippinarum) is a cultured bivalve with worldwide commercial importance, and diseases cause high economic losses. For this reason, interest in the immune genes in this species has recently increased. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application to study the gene transcription profiles of hemocytes from clams infected with V. alginolyticus through a time course. Results The complete set of sequences from R. philippinarum available in the public databases and the hemocyte sequences enriched in immune transcripts were assembled successfully. A total of 12,156 annotated sequences were used to construct the 8 ×15 k oligo-microarray. The microarray experiments yielded a total of 579 differentially expressed transcripts. Using the gene expression results, the associated Gene Ontology terms and the enrichment analysis, we found different response mechanisms throughout the experiment. Genes related to signaling, transcription and apoptosis, such as IL-17D, NF-κB or calmodulin, were typically expressed as early as 3 hours post-challenge (hpc), while characteristic immune genes, such as PGRPs, FREPs and defense proteins appeared later at 8 hpc. This immune-triggering response could have affected a high number of processes that seemed to be activated 24 hpc to overcome the Vibrio challenge, including the expression of many cytoskeleton molecules, which is indicative of the active movement of hemocytes. In fact functional studies showed an increment in apoptosis, necrosis or cell migration after the infection. Finally, 72 hpc, activity returned to normal levels, and more than 50% of the genes were downregulated in a negative feedback of all of the previously active processes. Conclusions Using a new version of the R. philippinarum oligo-microarray, a putative timing for the response against a Vibrio infection was established. The key point to overcome the challenge seemed to be 8 hours after the challenge, when we detected immune functions that could lead to the destruction of the pathogen and the activation of a wide variety of processes related to homeostasis and defense. These results highlight the importance of a fast response in bivalves and the effectiveness of their innate immune system.
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Affiliation(s)
| | | | | | | | | | | | | | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain.
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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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Suárez-Ulloa V, Fernández-Tajes J, Manfrin C, Gerdol M, Venier P, Eirín-López JM. Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds. Mar Drugs 2013; 11:4370-89. [PMID: 24189277 PMCID: PMC3853733 DOI: 10.3390/md11114370] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/27/2013] [Accepted: 10/09/2013] [Indexed: 12/26/2022] Open
Abstract
The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.
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Affiliation(s)
- Victoria Suárez-Ulloa
- Chromatin Structure and Evolution (CHROMEVOL) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA; E-Mail:
| | - Juan Fernández-Tajes
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; E-Mail:
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy; E-Mails: (C.M.); (M.G.)
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy; E-Mails: (C.M.); (M.G.)
| | - Paola Venier
- Department of Biology, University of Padova, Padova 35121, Italy; E-Mail:
| | - José M. Eirín-López
- Chromatin Structure and Evolution (CHROMEVOL) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-305-919-4000; Fax: +1-305-919-4030
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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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Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. CONSERVATION PHYSIOLOGY 2013; 1:cot009. [PMID: 27293593 PMCID: PMC4732435 DOI: 10.1093/conphys/cot009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 05/03/2023]
Abstract
Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the Pacific oyster (Crassostrea gigas), liquid chromatography coupled with tandem mass spectrometry was used to characterize the gill proteome. Using information from the recently published Pacific oyster genome, 1043 proteins were identified. Biological samples (n = 4) and corresponding technical replicates (three) were similar in both specific proteins identified and expression, as determined by normalized spectral abundance factor. A majority of the proteins identified (703) were present in all biological samples. Functional analysis of the protein repertoire illustrates that these proteins represent a wide range of biological processes, supporting the dynamic function of the gill. These insights are important for understanding environmental influences on the oyster, because the gill tissue acts as the interface between the oyster and its environment. In silico analysis indicated that this sequencing effort identified a large proportion of the complete gill proteome. Together, these data demonstrate that shotgun sequencing is a viable approach for biological discovery and will play an important role in future studies of oyster physiology.
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Affiliation(s)
- Emma Timmins-Schiffman
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
| | - Brook L. Nunn
- Genomic Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - David R. Goodlett
- Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
- Corresponding author: School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA. Tel: +1 206 685 3742.
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Sussarellu R, Dudognon T, Fabioux C, Soudant P, Moraga D, Kraffe E. Rapid mitochondrial adjustments in response to short-term hypoxia and re-oxygenation in the Pacific oyster Crassostrea gigas. J Exp Biol 2013; 216:1561-9. [DOI: 10.1242/jeb.075879] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Summary
As oxygen concentrations in marine coastal habitats can fluctuate rapidly and drastically, sessile marine organisms like the oyster Crassostrea gigas can experience marked and rapid oxygen variations. In this study, we investigated the responses of oyster gill mitochondria to short-term hypoxia (3 h and 12 h, at 1.7 mg O2 L-1) and subsequent re-oxygenation. Mitochondrial respiratory rates (state 3 and 4 stimulated by glutamate), phosphorylation efficiency (RCR ratio and ADP/O) were measured. Cytochrome c oxidase activity (CCO) and cytochrome concentrations (a, b, c1, c) were measured to investigate the rearrangements of respiratory chain subunits. The potential implication of an alternative oxidase (AOX) was investigated using an inhibitor of the respiratory chain (antimycin A) and through gene expression analysis in gills and digestive gland. Results indicate a down regulation of mitochondrial capacity, with 60% inhibition of respiratory rates after 12 h of hypoxia. RCR ratio remained stable, while ADP/O increased after 12 h of hypoxia and 1 h of re-oxygenation, suggesting increased phosphorylation efficiency. CCO showed a fast and remarkable increase of its catalytic activity only after 3 h of hypoxia. AOX mRNA levels showed similar patterns in gill and digestive gland, and were up regulated after 12 and 24 h of hypoxia and during re-oxygenation. Results suggest a set of controls in regulating mitochondrial functions in response to oxygen fluctuations and demonstrate the fast and extreme plasticity of oyster mitochondria in response to oxygen variations.
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Affiliation(s)
| | - Tony Dudognon
- UMR CNRS 6539-LEMAR, Université de Bretagne Occidentale, France
| | | | | | - Dario Moraga
- UMR CNRS 6539-LEMAR, Université de Bretagne Occidentale, France
| | - Edouard Kraffe
- UMR CNRS 6539-LEMAR, Université de Bretagne Occidentale, France
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Dheilly NM, Lelong C, Huvet A, Kellner K, Dubos MP, Riviere G, Boudry P, Favrel P. Gametogenesis in the Pacific oyster Crassostrea gigas: a microarrays-based analysis identifies sex and stage specific genes. PLoS One 2012; 7:e36353. [PMID: 22590533 PMCID: PMC3348941 DOI: 10.1371/journal.pone.0036353] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 04/03/2012] [Indexed: 11/19/2022] Open
Abstract
Background The Pacific oyster Crassostrea gigas (Mollusca, Lophotrochozoa) is an alternative and irregular protandrous hermaphrodite: most individuals mature first as males and then change sex several times. Little is known about genetic and phenotypic basis of sex differentiation in oysters, and little more about the molecular pathways regulating reproduction. We have recently developed and validated a microarray containing 31,918 oligomers (Dheilly et al., 2011) representing the oyster transcriptome. The application of this microarray to the study of mollusk gametogenesis should provide a better understanding of the key factors involved in sex differentiation and the regulation of oyster reproduction. Methodology/Principal Findings Gene expression was studied in gonads of oysters cultured over a yearly reproductive cycle. Principal component analysis and hierarchical clustering showed a significant divergence in gene expression patterns of males and females coinciding with the start of gonial mitosis. ANOVA analysis of the data revealed 2,482 genes differentially expressed during the course of males and/or females gametogenesis. The expression of 434 genes could be localized in either germ cells or somatic cells of the gonad by comparing the transcriptome of female gonads to the transcriptome of stripped oocytes and somatic tissues. Analysis of the annotated genes revealed conserved molecular mechanisms between mollusks and mammals: genes involved in chromatin condensation, DNA replication and repair, mitosis and meiosis regulation, transcription, translation and apoptosis were expressed in both male and female gonads. Most interestingly, early expressed male-specific genes included bindin and a dpy-30 homolog and female-specific genes included foxL2, nanos homolog 3, a pancreatic lipase related protein, cd63 and vitellogenin. Further functional analyses are now required in order to investigate their role in sex differentiation in oysters. Conclusions/Significance This study allowed us to identify potential markers of early sex differentiation in the oyster C. gigas, an alternative hermaphrodite mollusk. We also provided new highly valuable information on genes specifically expressed by mature spermatozoids and mature oocytes.
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Affiliation(s)
- Nolwenn M Dheilly
- Université de Caen Basse-Normandie, Biologie des Organismes Marins et des Ecosystèmes Associés, IBFA, SFR ICORE, Caen, France.
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Llera-Herrera R, García-Gasca A, Huvet A, Ibarra AM. Identification of a tubulin-α gene specifically expressed in testis and adductor muscle during stable reference gene selection in the hermaphrodite gonad of the lion's paw scallop Nodipecten subnodosus. Mar Genomics 2012; 6:33-44. [PMID: 22578657 DOI: 10.1016/j.margen.2012.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/05/2012] [Accepted: 03/09/2012] [Indexed: 01/03/2023]
Abstract
For non-model species, as many used for aquaculture, with minimal or no genomic information, relative quantification of gene expression studies requires preliminary research including the isolation of potential reference genes and the identification of those stably expressed under the biological conditions of interest. Here we report on the isolation of five partial gene sequences from gonad tissue cDNA in the functional hermaphrodite scallop Nodipecten subnodosus to be evaluated as reference genes: 18S-rRNA, riboprotein l8 (rp-l8), actin-β (act-β), elongation factor 1α (ef-1α) and alpha-tubulin-α (tub-α). We found that 18S-rRNA was stably expressed independently of the priming method used to reverse transcribe RNA to cDNA, oligo-dT or random hexamer. Stability analysis for the five putative reference genes with geNorm and NormFinder indicated that 18S together with rp-l8 were the most stable genes for normalization of gene expression during gonad development in both, male and female sexual regions of the hermaphrodite N. subnodosus. The least stable gene was tub-α, showing a biased expression profile between sexual regions of the gonad, therefore this gene was analyzed thereafter as a target gene together with vitellogenin (vit) and a DEAD-box RNA helicase (dbx) gene. Relative expression, estimated by normalization with the combination of 18S and rp-l8 as reference genes, indicated that as gonad development advanced two of the target genes were up-regulated, tub-α in the male region and vit in the female region. Whereas an increased expression was expected during development for vit for its known role in vitellogenesis, the increased expression of tub-α in the male sexual region was unexpected, and pointed toward this gene being a testis-specific α-tubulin isotype. Further analyses of gene expression among tissues indicated that tub-α is specifically and highly expressed in the male gonad, although expression in adductor muscle was also observed at significantly lower levels. The existence of testis specific α- and β-tubulins has been previously reported in other taxa, relating their function to sperm axoneme formation. Tissue-specific tubulin genes, particularly their promoters, have recently found an application as native promoters for transgene tissue-specific expression in research and reproductive control of insect plagues. The third target gene, a putative member of the DEAD-box RNA helicase family (dbx), showed no changes in expression during gonad development or between sexual regions, therefore it was chosen to discuss the different statistical inferences resulting from the arbitrary use of 'randomly chosen' reference genes when normalizing gene expression.
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Affiliation(s)
- Raúl Llera-Herrera
- Centro de Investigaciones Biológicas del Noroeste, S.C. Mar Bermejo 195, Col. Playa Palo de Sta. Rita, La Paz B.C.S. 23090, Mexico
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