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Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
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Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
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Examination of the potential roles of insulin-like peptide receptor in regulating the growth of Manila clam Ruditapes philippinarum. Comp Biochem Physiol A Mol Integr Physiol 2022; 274:111315. [PMID: 36089185 DOI: 10.1016/j.cbpa.2022.111315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/22/2022]
Abstract
The role of insulin/insulin-like growth factor (IGF) signaling pathway in the growth regulation of marine invertebrates has not been fully studied. In this study, the economically important species Ruditapes philippinarum was sacrificed to clarify the role of IGF system in the growth regulation of R. philippinarum by real-time quantitative PCR. Systematic bioinformatics analysis can identify the major genes of IGF signaling pathway and insulin-like peptide receptor (ILPR) - mediated signaling pathway in R. philippinarum. The expression levels of IGF and its downstream signaling pathway genes in larger clams were significantly higher than those in small clams, indicating that they were involved in the growth regulation of R. philippinarum. These results suggest that IGF signaling pathway and ILPR mediated signaling pathway to regulate the growth of R. philippinarum.
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Adema CM. Sticky problems: extraction of nucleic acids from molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200162. [PMID: 33813891 DOI: 10.1098/rstb.2020.0162] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. DNA extraction methods that employ the detergent hexadecyltrimethylammoniumbromide (CTAB) to remove these contaminants importantly facilitate molecular-level study of molluscs. Molluscan pigments may stain DNA samples and interfere with spectrophotometry, necessitating gel electrophoresis or fluorometry for accurate quantification. RNA can reliably be extracted but the 'hidden break' in 28S rRNA of molluscs (like most protostomes) causes 18S and 28S rRNA fragments to co-migrate electrophoretically. This challenges the standard quality control based on the ratio of 18S and 28S rRNA, developed for deuterostome animals. High-AT content in molluscan rRNA prevents the effective purification of polyadenylated mRNA. Awareness of these matters aids the continuous expansion of molecular malacology, enabling work also with museum specimens and next-generation sequencing, with the latter imposing unprecedented demands on DNA quality. Alternative methods to extract nucleic acids from molluscs are available from literature and, importantly, from communications with others who study the molecular biology of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87112, USA
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Nature more than nurture affects the growth rate of mussels. Sci Rep 2020; 10:3539. [PMID: 32103079 PMCID: PMC7044158 DOI: 10.1038/s41598-020-60312-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/10/2020] [Indexed: 11/21/2022] Open
Abstract
We tested the hypothesis that environmental trophic conditions prominent during the growing period (nurture conditions) can modify the differing physiological profiles between fast (F)- and slow (S)-growing juveniles of the mussel Mytilus galloprovincialis. Approximately 200 individuals were fed a high organic content diet dosed below the pseudofaeces threshold (BP), whereas another 200 were fed a low organic content diet dosed above the pseudofaeces threshold (AP), forcing them to maintain a continuous production of pseudofaeces. After 3 months, F and S individuals in each rearing condition were selected and used in feeding experiments. We measured the physiological parameters of the energy balance of selected F and S mussels fed on 4 different diets and tested the effects of the rearing condition (BP vs AP) and growth condition (F vs S) upon the physiological variables. Irrespective of the rearing condition, F-mussels attained higher values of scope for growth with the four experimental diets due to their capacity to display higher clearance rates and preingestive selection efficiencies. F-individuals also had higher gill-surface areas than S individuals. We discussed the role of the gills in determining inter-individual growth rate differences in the mussel.
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Jiang S, Miao J, Wang X, Liu P, Pan L. Inhibition of growth in juvenile manila clam Ruditapes philippinarum: Potential adverse outcome pathway of TBBPA. CHEMOSPHERE 2019; 224:588-596. [PMID: 30844590 DOI: 10.1016/j.chemosphere.2019.02.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/09/2019] [Accepted: 02/23/2019] [Indexed: 06/09/2023]
Abstract
Tetrabromobisphenol A (TBBPA) is ubiquitous and its contents showing an increasing trend in the coastal environment. In order to investigate the effects of TBBPA on marine bivalves, juvenile manila clams Ruditapes phillipinarum were exposed to TBBPA for 28 days. The results showed that shell growth rate of juvenile clams after exposure to 62.5-1000 μg L-1 TBBPA for 28 d were significantly inhibited (p < 0.05). Then in order to link the changes in filtration rate, mRNA expression of insulin-like growth factor homologue (IGF) and tissue thyroid hormone (TH) contents to growth, juvenile clams were exposed to 62.5 and 500 μg L-1 TBBPA for 14 days. The transcriptional levels of neuroendocrine signals (NPF and insulin homologue) associated with filter feeding regulation, and genes of TH synthesis-related enzymes were also examined. The results showed that filtration rates was significantly reduced to 44.1% and 14% of controls after 14 d of exposure. In parallel, exposure to TBBPA significantly increased the expression levels of insulin which may elicit the filter feeding inhibition. TBBPA exposure caused alterations in tissue content of THs and mRNA expression of TH synthesis-related enzymes. However, the data showed increased T3 content, T3/T4 ratio and mRNA expression of IGF. These data demonstrated that the most important key event of TBBPA could be linked to growth impairment in juveniles was the reduction of filtration rate. These results provide a robust framework towards revealing the underlying mechanism of the growth inhibition caused by TBBPA on bivalves and understanding the adverse outcome pathway across taxonomic phyla.
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Affiliation(s)
- Shanshan Jiang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, PR China
| | - Jingjing Miao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, PR China.
| | - Xin Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, PR China
| | - Peipei Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, PR China
| | - Luqing Pan
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, PR China
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