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Aagaard A, Bechsgaard J, Sørensen JG, Sandfeld T, Settepani V, Bird TL, Lund MB, Malmos KG, Falck-Rasmussen K, Darolti I, Nielsen KL, Johannsen M, Vosegaard T, Tregenza T, Verhoeven KJF, Mank JE, Schramm A, Bilde T. Molecular Mechanisms of Temperature Tolerance Plasticity in an Arthropod. Genome Biol Evol 2024; 16:evae165. [PMID: 39058286 DOI: 10.1093/gbe/evae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
How species thrive in a wide range of environments is a major focus of evolutionary biology. For many species, limited genetic diversity or gene flow among habitats means that phenotypic plasticity must play an important role in their capacity to tolerate environmental heterogeneity and to colonize new habitats. However, we have a limited understanding of the molecular components that govern plasticity in ecologically relevant phenotypes. We examined this hypothesis in a spider species (Stegodyphus dumicola) with extremely low species-wide genetic diversity that nevertheless occupies a broad range of thermal environments. We determined phenotypic responses to temperature stress in individuals from four climatic zones using common garden acclimation experiments to disentangle phenotypic plasticity from genetic adaptations. Simultaneously, we created data sets on multiple molecular modalities: the genome, the transcriptome, the methylome, the metabolome, and the bacterial microbiome to determine associations with phenotypic responses. Analyses of phenotypic and molecular associations reveal that acclimation responses in the transcriptome and metabolome correlate with patterns of phenotypic plasticity in temperature tolerance. Surprisingly, genes whose expression seemed to be involved in plasticity in temperature tolerance were generally highly methylated contradicting the idea that DNA methylation stabilizes gene expression. This suggests that the function of DNA methylation in invertebrates varies not only among species but also among genes. The bacterial microbiome was stable across the acclimation period; combined with our previous demonstrations that the microbiome is temporally stable in wild populations, this is convincing evidence that the microbiome does not facilitate plasticity in temperature tolerance. Our results suggest that population-specific variation in temperature tolerance among acclimation temperatures appears to result from the evolution of plasticity in mainly gene expression.
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Affiliation(s)
- Anne Aagaard
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Jesper Bechsgaard
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Jesper Givskov Sørensen
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Tobias Sandfeld
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Virginia Settepani
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Tharina L Bird
- General Entomology, DITSONG: National Museum of Natural History, Pretoria, South Africa
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Arachnology and Myriapodology, National Museum of Namibia, Windhoek, Namibia
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Kirsten Gade Malmos
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Kasper Falck-Rasmussen
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mogens Johannsen
- Department of Forensic Medicine, Aarhus University, Aarhus N, Denmark
| | - Thomas Vosegaard
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Tom Tregenza
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR109FE, UK
| | - Koen J F Verhoeven
- Terrestrial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Trine Bilde
- Section for Genetics, Ecology and Evolution, Centre for EcoGenetics, Department of Biology, Aarhus University, Aarhus C, Denmark
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR109FE, UK
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Risha KS, Rasal KD, Reang D, Iquebal MA, Sonwane A, Brahmane M, Chaudhari A, Nagpure N. DNA Methylation Profiling in Genetically Selected Clarias magur (Hamilton, 1822) Provides Insights into the Epigenetic Regulation of Growth and Development. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:776-789. [PMID: 39037491 DOI: 10.1007/s10126-024-10346-4] [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: 05/29/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals.
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Affiliation(s)
- K Shasti Risha
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India.
| | - Dhalongsaih Reang
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Arvind Sonwane
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Manoj Brahmane
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Naresh Nagpure
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
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3
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Viña-Feás A, Temes-Rodríguez J, Vidal-Capón A, Novas S, Rodríguez-Castro J, Pequeño-Valtierra A, Pasantes JJ, Tubío JMC, Garcia-Souto D. Unravelling epigenetic mechanisms in Cerastoderma edule genome: a comparison of healthy and neoplastic cockles. Mol Genet Genomics 2024; 299:58. [PMID: 38789628 PMCID: PMC11126487 DOI: 10.1007/s00438-024-02148-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/28/2024] [Indexed: 05/26/2024]
Abstract
Cancer is a multifaceted genetic disease characterized by the acquisition of several essential hallmarks. Notably, certain cancers exhibit horizontal transmissibility, observed across mammalian species and diverse bivalves, the latter referred to as hemic neoplasia. Within this complex landscape, epigenetic mechanisms such as histone modifications and cytosine methylation emerge as fundamental contributors to the pathogenesis of these transmissible cancers. Our study delves into the epigenetic landscape of Cerastoderma edule, focusing on whole-genome methylation and hydroxymethylation profiles in heathy specimens and transmissible neoplasias by means of Nanopore long-read sequencing. Our results unveiled a global hypomethylation in the neoplastic specimens compared to their healthy counterparts, emphasizing the role of DNA methylation in these tumorigenic processes. Furthermore, we verified that intragenic CpG methylation positively correlated with gene expression, emphasizing its role in modulating transcription in healthy and neoplastic cockles, as also highlighted by some up-methylated oncogenic genes. Hydroxymethylation levels were significantly more elevated in the neoplastic samples, particularly within satellites and complex repeats, likely related to structural functions. Additionally, our analysis also revealed distinct methylation and activity patterns in retrotransposons, providing additional insights into bivalve neoplastic processes. Altogether, these findings contribute to understanding the epigenetic dynamics of bivalve neoplasias and shed light on the roles of DNA methylation and hydroxymethylation in tumorigenesis. Understanding these epigenetic alterations holds promise for advancing our broader understanding of cancer epigenetics.
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Affiliation(s)
- Alejandro Viña-Feás
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Javier Temes-Rodríguez
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Samuel Novas
- Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Jorge Rodríguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | | | - Jose M C Tubío
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel Garcia-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Department of Biological Sciences, School of Environment, Arts and Society, College of Arts, Sciences & Education (CASE), Florida International University, Miami, FL, USA.
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Sun D, Yu H, Kong L, Liu S, Xu C, Li Q. The role of DNA methylation reprogramming during sex determination and sex reversal in the Pacific oyster Crassostrea gigas. Int J Biol Macromol 2024; 259:128964. [PMID: 38219938 DOI: 10.1016/j.ijbiomac.2023.128964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/19/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024]
Abstract
DNA methylation is instrumental in vertebrate sex reversal. However, the mechanism of DNA methylation regulation regarding sex reversal in invertebrates is unclear. In this study, we used whole genome bisulfite sequencing (WGBS) to map single-base resolution methylation profiles of the Pacific oyster, including female-to-male (FMa-to-FMb) and male-to-female (MFa-to-MFb) sex reversal, as well as sex non-reversed males and females (MMa-to-MMb and FFa-to-FFb). The results showed that global DNA methylation levels increase during female-to-male sex reversals, with a particular increase in the proportion of high methylation levels (mCGs >0.75) and a decrease in the proportion of intermediate methylation levels (0.25 < mCGs <0.75). This increase in DNA methylation was mainly associated with the elevated expression of DNA methylase genes. Genome-wide methylation patterns of females were accurately remodeled to those of males after sex reversal, while the opposite was true for the male-to-female reversal. Those findings directly indicate that alterations in DNA methylation play a significant role in sex reversal in Pacific oysters. Comparative analysis of the DNA methylomes of pre- and post- sex reversal gonadal tissues (FMb-vs-FMa or MFb-vs-MFa) revealed that differentially methylated genes were mainly involved in the biological processes of sex determination or gonadal development. However critical genes such as Dmrt1, Foxl2 and Sox-like, which are involved in the putative sex determination pathway in Pacific oysters, showed almost an absence of methylation modifications, varying greatly from vertebrates. Additionally, comparative analysis of the DNA methylomes of sexual reversal and sex non-reversal (FMa-vs-FFa or MFa-vs-MMa) revealed that heat shock protein genes, such as Hsp68-like and Hsp70B, were important for the occurrence of sex reversal. These findings shed light on the epigenetic mechanisms underlying the maintenance of gonadal plasticity and the reversal of organ architecture in oysters.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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5
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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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6
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Hart SFM, Yonemitsu MA, Giersch RM, Garrett FES, Beal BF, Arriagada G, Davis BW, Ostrander EA, Goff SP, Metzger MJ. Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia. NATURE CANCER 2023; 4:1561-1574. [PMID: 37783804 PMCID: PMC10663159 DOI: 10.1038/s43018-023-00643-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 08/29/2023] [Indexed: 10/04/2023]
Abstract
Transmissible cancers are infectious parasitic clones that metastasize to new hosts, living past the death of the founder animal in which the cancer initiated. We investigated the evolutionary history of a cancer lineage that has spread though the soft-shell clam (Mya arenaria) population by assembling a chromosome-scale soft-shell clam reference genome and characterizing somatic mutations in transmissible cancer. We observe high mutation density, widespread copy-number gain, structural rearrangement, loss of heterozygosity, variable telomere lengths, mitochondrial genome expansion and transposable element activity, all indicative of an unstable cancer genome. We also discover a previously unreported mutational signature associated with overexpression of an error-prone polymerase and use this to estimate the lineage to be >200 years old. Our study reveals the ability for an invertebrate cancer lineage to survive for centuries while its genome continues to structurally mutate, likely contributing to the evolution of this lineage as a parasitic cancer.
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Affiliation(s)
- Samuel F M Hart
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marisa A Yonemitsu
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | | | - Brian F Beal
- Division of Environmental and Biological Sciences, University of Maine at Machias, Machias, ME, USA
- Downeast Institute, Beals, ME, USA
| | - Gloria Arriagada
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University School of Veterinary Medicine, College Station, TX, USA
- Department of Small Animal Clinical Sciences, Texas A&M University School of Veterinary Medicine, College Station, TX, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Michael J Metzger
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
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Perez M, Aroh O, Sun Y, Lan Y, Juniper SK, Young CR, Angers B, Qian PY. Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes. Mol Biol Evol 2023; 40:msad172. [PMID: 37494294 PMCID: PMC10414810 DOI: 10.1093/molbev/msad172] [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: 02/24/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.
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Affiliation(s)
- Maeva Perez
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Oluchi Aroh
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Stanley Kim Juniper
- School of Earth and Ocean Sciences, University of Victoria, Victoria, Canada
| | | | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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Venkataraman YR, White SJ, Roberts SB. Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification. BMC Genomics 2022; 23:556. [PMID: 35927609 PMCID: PMC9351233 DOI: 10.1186/s12864-022-08781-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/13/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) - a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture- to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. RESULTS Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination - commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. CONCLUSIONS Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation.
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Affiliation(s)
- Yaamini R Venkataraman
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA.
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA.
| | - Samuel J White
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA, USA
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Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
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Männer L, Schell T, Provataris P, Haase M, Greve C. Inference of DNA methylation patterns in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200166. [PMID: 33813896 DOI: 10.1098/rstb.2020.0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Given the evolutionary age and morphological diversity of molluscs, we expected to find evidence for diverse methylation patterns. Our inferences suggest that molluscs possess substantial levels of DNA methylation in gene bodies as a rule. Yet, we found deviations from this general picture with regard to (i) the CpG observed/expected distributions indicating a reduction in DNA methylation in certain groups and (ii) the completeness of the DNMT toolkit. Reductions were evident in Caudofoveata, Solenogastres, Polyplacophora, Monoplacophora, as well as Scaphopoda. Heterobranchia and Oegopsida were remarkable as they lacked DNMT3, usually responsible for de novo methylation, yet showed signs of DNA methylation. Our survey may serve as guidance for direct empirical analyses of DNA methylation in 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)
- Lisa Männer
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.,Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Martin Haase
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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12
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105217. [PMID: 33276167 DOI: 10.1016/j.marenvres.2020.105217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 06/12/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122, NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
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13
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105214. [PMID: 33221553 DOI: 10.1016/j.marenvres.2020.105214] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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Gurr SJ, Vadopalas B, Roberts SB, Putnam HM. Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater. CONSERVATION PHYSIOLOGY 2020; 8:coaa024. [PMID: 32274068 PMCID: PMC7125045 DOI: 10.1093/conphys/coaa024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/12/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 μatm) or elevated (~2400 μatm) pCO2 treatments and in common, ambient conditions, 5 months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories; however, clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after 5 months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after 5 months in ambient conditions. Early exposure to low pH appears to trigger carryover effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam.
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Affiliation(s)
- Samuel J Gurr
- College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
| | - Brent Vadopalas
- Washington Sea Grant, University of Washington, 3716 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA 98105, USA
| | - Hollie M Putnam
- College of the Environment and Life Sciences, University of Rhode Island, 120 Flagg Rd, Kingston, RI 02881, USA
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15
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Spencer LH, Venkataraman YR, Crim R, Ryan S, Horwith MJ, Roberts SB. Carryover effects of temperature and pCO 2 across multiple Olympia oyster populations. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02060. [PMID: 31863716 DOI: 10.1002/eap.2060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/07/2019] [Accepted: 10/21/2019] [Indexed: 05/20/2023]
Abstract
Predicting how populations will respond to ocean change across generations is critical to effective conservation of marine species. One emerging factor is the influence of parental exposures on offspring phenotype, known as intergenerational carryover effects. Parental exposure may deliver beneficial or detrimental characteristics to offspring that can influence larval recruitment patterns, thus shaping how populations and community structure respond to ocean change. Impacts of adult exposure to elevated winter temperature and pCO2 on reproduction and offspring viability were examined in the Olympia oyster (Ostrea lurida) using three populations of adult, hatchery-reared O. lurida, plus an additional cohort spawned from one of the populations. Oysters were sequentially exposed to elevated temperature (+4°C, at 10°C), followed by elevated pCO2 (+2,204 μatm, at 3,045 μatm) during winter months. Male gametes were more developed after elevated temperature exposure and less developed after high pCO2 exposure, but there was no impact on female gametes or sex ratios. Oysters previously exposed to elevated winter temperature released larvae earlier, regardless of pCO2 exposure. Those exposed to elevated winter temperature as a sole treatment released more larvae on a daily basis but, when also exposed to high pCO2 , there was no effect. These combined results indicate that elevated winter temperature accelerates O. lurida spermatogenesis, resulting in earlier larval release and increased production, with elevated pCO2 exposure negating effects of elevated temperature. Altered recruitment patterns may therefore follow warmer winters due to precocious spawning, but these effects may be masked by coincidental high pCO2 . Offspring were reared in common conditions for 1 yr, then deployed for 3 months in four estuarine bays with distinct environmental conditions. Offspring of parents exposed to elevated pCO2 had higher survival rates in two of the four bays. This carryover effect demonstrates that parental conditions can have substantial ecologically relevant impacts that should be considered when predicting impacts of environmental change. Furthermore, Olympia oysters may be more resilient in certain environments when progenitors are pre-conditioned in stressful conditions. Combined with other recent studies, our work suggests that the Olympia may be more equipped than other oysters for the challenge of a changing ocean.
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Affiliation(s)
- Laura H Spencer
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, 98105, USA
| | - Yaamini R Venkataraman
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, 98105, USA
| | - Ryan Crim
- Puget Sound Restoration Fund, 8001 NE Day Road West, Bainbridge Island, Washington, 98110, USA
| | - Stuart Ryan
- Puget Sound Restoration Fund, 8001 NE Day Road West, Bainbridge Island, Washington, 98110, USA
| | - Micah J Horwith
- Washington State Department of Natural Resources, 1111 Washington Street SE, MS 47027, Olympia, Washington, 98504, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, Washington, 98105, USA
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Epigenetic patterns associated with an ascidian invasion: a comparison of closely related clades in their native and introduced ranges. Sci Rep 2019; 9:14275. [PMID: 31582771 PMCID: PMC6776620 DOI: 10.1038/s41598-019-49813-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 08/29/2019] [Indexed: 12/12/2022] Open
Abstract
Environmentally induced epigenetic modifications have been proposed as one mechanism underlying rapid adaptive evolution of invasive species. Didemnum vexillum is an invasive colonial ascidian that has established in many coastal waters worldwide. Phylogenetic analyses have revealed that D. vexillum populations consist of two distinct clades; clade B appears to be restricted to the native range (Japan), whereas clade A is found in many regions throughout the world, including New Zealand. The spread of D. vexillum clade A suggests that it might be intrinsically more invasive than clade B, despite low levels of genetic diversity compared to populations from the native region. This study investigated whether D. vexillum clade A exhibits epigenetic signatures (specifically differences in DNA methylation) associated with invasiveness. Global DNA methylation patterns were significantly different between introduced clade A colonies, and both clades A and B in the native range. Introduced colonies also showed a significant reduction in DNA methylation levels, which could be a mechanism for increasing phenotypic plasticity. High levels of DNA methylation diversity were maintained in the introduced population, despite reduced levels of genetic diversity, which may allow invasive populations to respond quickly to changes in new environments. Epigenetic changes induced during the invasion process could provide a means for rapid adaptation despite low levels of genetic variation in introduced populations.
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17
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Li Y, Zhang L, Li Y, Li W, Guo Z, Li R, Hu X, Bao Z, Wang S. Dynamics of DNA Methylation and DNMT Expression During Gametogenesis and Early Development of Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:196-205. [PMID: 30680591 DOI: 10.1007/s10126-018-09871-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
DNA methylation reprograms during gametogenesis and embryo development, which is essential for germ cell specification and genomic imprinting in mammals. Corresponding process remains poorly investigated in molluscs. Here, we examined global DNA methylation level in the gonads of scallop Patinopecten yessoensis during gametogenesis and in embryos/larvae at different stages. DNA methylation level fluctuates during gametogenesis and early development, peaking at proliferative stage of ovary, growing stage of testis, and in blastulae. To understand the mechanisms underlying these changes, we conducted genome-wide characterization of DNMT family and investigated their expression profiles based on transcriptomes and in situ hybridization. Three genes were identified, namely PyDNMT1, PyDNMT2, and PyDNMT3. Expression of PyDnmt3 agrees with DNA methylation level during oogenesis and early development, suggesting PyDNMT3 may participate in de novo DNA methylation that occurs mainly at proliferative stage of ovary and testis, and in blastulae and gastrulae. PyDnmt1 expression is positively correlated with DNA methylation level during spermatogenesis, and is higher at maturation stage of ovary and in 2-8 cell embryos than other stages, implying possible involvement of PyDNMT1 in DNA methylation maintenance during meiosis and embryonic development. This study will facilitate better understanding of the developmental epigenetic reprogramming in bivalve molluscs.
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Affiliation(s)
- Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Wanru Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Zhenyi Guo
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, Shandong, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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Ardura A, Clusa L, Zaiko A, Garcia-Vazquez E, Miralles L. Stress related epigenetic changes may explain opportunistic success in biological invasions in Antipode mussels. Sci Rep 2018; 8:10793. [PMID: 30018391 PMCID: PMC6050280 DOI: 10.1038/s41598-018-29181-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
Different environmental factors could induce epigenetic changes, which are likely involved in the biological invasion process. Some of these factors are driven by humans as, for example, the pollution and deliberate or accidental introductions and others are due to natural conditions such as salinity. In this study, we have analysed the relationship between different stress factors: time in the new location, pollution and salinity with the methylation changes that could be involved in the invasive species tolerance to new environments. For this purpose, we have analysed two different mussels' species, reciprocally introduced in antipode areas: the Mediterranean blue mussel Mytilus galloprovincialis and the New Zealand pygmy mussel Xenostrobus securis, widely recognized invaders outside their native distribution ranges. The demetylathion was higher in more stressed population, supporting the idea of epigenetic is involved in plasticity process. These results can open a new management protocols, using the epigenetic signals as potential pollution monitoring tool. We could use these epigenetic marks to recognise the invasive status in a population and determine potential biopollutants.
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Affiliation(s)
- Alba Ardura
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain.
| | - Laura Clusa
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
- Marine Research Institute, Klaipeda University, H. Manto 84, Klaipeda, 92294, Lithuania
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain
| | - Laura Miralles
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Spain
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Gavery MR, Roberts SB. Epigenetic considerations in aquaculture. PeerJ 2017; 5:e4147. [PMID: 29230373 PMCID: PMC5723431 DOI: 10.7717/peerj.4147] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
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21
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Portet A, Pinaud S, Tetreau G, Galinier R, Cosseau C, Duval D, Grunau C, Mitta G, Gourbal B. Integrated multi-omic analyses in Biomphalaria-Schistosoma dialogue reveal the immunobiological significance of FREP-SmPoMuc interaction. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:16-27. [PMID: 28257854 DOI: 10.1016/j.dci.2017.02.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/23/2017] [Accepted: 02/26/2017] [Indexed: 05/16/2023]
Abstract
The fresh water snail Biomphalaria glabrata is one of the vectors of the trematode pathogen Schistosoma mansoni, which is one of the agents responsible of human schistosomiasis. In this host-parasite interaction, co-evolutionary dynamic results into an infectivity mosaic known as compatibility polymorphism. Integrative approaches including large scale molecular approaches have been conducted in recent years to improve our understanding of the mechanisms underlying compatibility. This review presents the combination of integrated Multi-Omic approaches leading to the discovery of two repertoires of polymorphic and/or diversified interacting molecules: the parasite antigens S. mansoni polymorphic mucins (SmPoMucs) and the B. glabrata immune receptors fibrinogen-related proteins (FREPs). We argue that their interactions may be major components for defining the compatible/incompatible status of a specific snail/schistosome combination.
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Affiliation(s)
- Anaïs Portet
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Silvain Pinaud
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Guillaume Tetreau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Richard Galinier
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Céline Cosseau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - David Duval
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Christoph Grunau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Guillaume Mitta
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Benjamin Gourbal
- Univ. Perpignan Via Domitia, IHPE UMR 5244, IFREMER, Univ. Montpellier, F-66860 Perpignan, France.
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22
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Dimond JL, Gamblewood SK, Roberts SB. Genetic and epigenetic insight into morphospecies in a reef coral. Mol Ecol 2017; 26:5031-5042. [DOI: 10.1111/mec.14252] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
- Shannon Point Marine Center Western Washington University Anacortes WA USA
| | | | - Steven B. Roberts
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
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Farias ND, de Oliveira NFP, da Silva PM. Perkinsus infection is associated with alterations in the level of global DNA methylation of gills and gastrointestinal tract of the oyster Crassostrea gasar. J Invertebr Pathol 2017; 149:76-81. [PMID: 28800971 DOI: 10.1016/j.jip.2017.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
Bivalves are filter feeders that obtain food from seawater that may contain infectious agents, such as the protozoan parasites Perkinsus marinus and P. olseni that are associated with massive mortalities responsible for losses in the aquaculture industry. Despite all physical and chemical barriers, microorganisms cross epithelia and infect host tissues to cause pathologies. Epigenetics mechanisms play important roles in a variety of human processes, from embryonic development to cell differentiation and growth. It is currently emerging as crucial mechanism involved in modulation of host-parasite interactions and pathogenesis, promoting discovery of targets for drug treatment. In bivalves, little is known about epigenetic mechanism in host parasite interactions. The objective of the present study was to evaluate the effect of Perkinsus sp. infections on DNA methylation levels in tissues of Crassostrea gasar oysters. Samples were collected in 2015 and 2016 in the Mamanguape River estuary (PB). Oyster gills were removed and used for Perkinsus sp. DIAGNOSIS Gills (G) and gastrointestinal tract (GT), as well as cultured P. marinus trophozoites were preserved in 95% ethanol for DNA extractions. DNA methylation levels were estimated from G and GT tissues of uninfected (n=60) and infected oysters (n=60), and from P. marinus trophozoites, by ELISA assays. Results showed that the mean prevalence of Perkinsus sp. infections was high (87.3%) in 2015 and moderate (59.6%) in 2016. DNA methylation levels of G and GT tissues were significantly lower in infected oyster than in uninfected oysters, suggesting that infections are associated with hypomethylation. Methylation level was significantly higher in G than in GT tissues, indicating a likely tissue-specific mechanism. P. marinus trophozoites showed 33% methylation. This was the first study that confirms alterations of DNA methylation in two tissues of C. gasar oysters in association with Perkinsus sp. infections.
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Affiliation(s)
- Natanael Dantas Farias
- Laboratório de Imunologia e Patologia de Invertebrados, Departamento de Biologia Molecular, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil.
| | - Naila Francis Paulo de Oliveira
- Laboratório de Genética Molecular Humana, Departamento de Biologia Molecular, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil.
| | - Patricia Mirella da Silva
- Laboratório de Imunologia e Patologia de Invertebrados, Departamento de Biologia Molecular, Universidade Federal da Paraíba, CEP 58051-900, João Pessoa, PB, Brazil.
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24
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Bachère E, Barranger A, Bruno R, Rouxel J, Menard D, Piquemal D, Akcha F. Parental diuron-exposure alters offspring transcriptome and fitness in Pacific oyster Crassostrea gigas. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:51-58. [PMID: 28388477 DOI: 10.1016/j.ecoenv.2017.03.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
One of the primary challenges in ecotoxicology is to contribute to the assessment of the ecological status of ecosystems. In this study, we used Pacific oyster Crassostrea gigas to explore the effects of a parental exposure to diuron, a herbicide frequently detected in marine coastal environments. The present toxicogenomic study provides evidence that exposure of oyster genitors to diuron during gametogenesis results in changes in offspring, namely, transcriptomic profile alterations, increased global DNA methylation levels and reduced growth and survival within the first year of life. Importantly, we highlighted the limitations to identify particular genes or gene expression signatures that could serve as biomarkers for parental herbicide-exposure and further for multigenerational and transgenerational effects of specific chemical stressors. By analyzing samples from two independent experiments, we demonstrated that, due to complex confounding effects with both tested solvent vehicles, diuron non-specifically affected the offspring transcriptome. These original results question the potential development of predictive genomic tools for detecting specific indirect impacts of contaminants in environmental risk assessments. However, our results indicate that chronic environmental exposure to diuron over several generations may have significant long term impacts on oyster populations with adverse health outcomes.
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Affiliation(s)
- Evelyne Bachère
- Ifremer, UMR 5244, IHPE Interactions-Hosts-Pathogens-Environments, UPVD, CNRS, Université de Montpellier, CC 80, F-34095 Montpellier, France.
| | - Audrey Barranger
- Ifremer, Laboratoire d'Ecotoxicologie, Rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 03, France
| | - Roman Bruno
- Acobiom, 1682 rue de la Valsière, CS 77394 Cap Delta Biopole Euromédecine II, 34184 Montpellier Cedex 04, France
| | - Julien Rouxel
- Ifremer, Laboratoire d'Ecotoxicologie, Rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 03, France
| | - Dominique Menard
- Ifremer, Laboratoire d'Ecotoxicologie, Rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 03, France
| | - David Piquemal
- Acobiom, 1682 rue de la Valsière, CS 77394 Cap Delta Biopole Euromédecine II, 34184 Montpellier Cedex 04, France; Diag4Zoo, 1 rue des Loutres, 34170 Montpellier, France
| | - Farida Akcha
- Ifremer, Laboratoire d'Ecotoxicologie, Rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 03, France
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Dynamics of DNA methylomes underlie oyster development. PLoS Genet 2017; 13:e1006807. [PMID: 28594821 PMCID: PMC5481141 DOI: 10.1371/journal.pgen.1006807] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 06/22/2017] [Accepted: 05/08/2017] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model, the oyster Crassostrea gigas, from the egg to the completion of organogenesis. Large-scale methylation maps reveal that the oyster genome displays a succession of methylated and non methylated regions, which persist throughout development. Differentially methylated regions (DMRs) are strongly regulated during cleavage and metamorphosis. The distribution and levels of methylated DNA within genomic features (exons, introns, promoters, repeats and transposons) show different developmental lansdscapes marked by a strong increase in the methylation of exons against introns after metamorphosis. Kinetics of methylation in gene-bodies correlate to their transcription regulation and to distinct functional gene clusters, and DMRs at cleavage and metamorphosis bear the genes functionally related to these steps, respectively. This study shows that DNA methylome dynamics underlie development through transcription regulation in the oyster, a lophotrochozoan species. To our knowledge, this is the first demonstration of such epigenetic regulation outside vertebrates and ecdysozoan models, bringing new insights into the evolution and the epigenetic regulation of developmental processes. Elucidating the mechanisms which govern the development of multicellular animals and their evolution is a fundamental task. Epigenetic mechanisms like DNA methylation have recently emerged as critical regulators of mammalian development through the control of genes that determine the identity of cells and the transmission of parental imprints. In invertebrates however, DNA is mostly unmethylated and does not play a role in development except in the peculiar case of social insects. Therefore the significance of DNA methylation in development is thought to be restricted to vertebrates, and thereby considered a recent evolutionary acquisition, and the situation in more distant organisms is unknown. Here we investigated the dynamics of genome-wide DNA methylation patterns in a mollusc, the oyster C. gigas, throughout its development. We found that the dynamics of DNA methylation correspond to the expression dynamics of distinct functional gene clusters that control two critical development steps, cleavage and metamorphosis, and we provide insights into the underlying molecular mechanisms in a non-vertebrate species. These findings challenge the present considerations on the evolution of developmental processes and their epigenetic regulation, and open a new area of research in molecular and developmental biology in invertebrates.
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Gonzalez-Romero R, Suarez-Ulloa V, Rodriguez-Casariego J, Garcia-Souto D, Diaz G, Smith A, Pasantes JJ, Rand G, Eirin-Lopez JM. Effects of Florida Red Tides on histone variant expression and DNA methylation in the Eastern oyster Crassostrea virginica. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 186:196-204. [PMID: 28315825 DOI: 10.1016/j.aquatox.2017.03.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 06/06/2023]
Abstract
Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and annual losses in excess of $40 million. The ability of marine organisms to cope with environmental stressors (including those produced during HABs) is influenced by genetic and epigenetic mechanisms, the latter resulting in phenotypic changes caused by heritable modifications in gene expression, without involving changes in the genetic (DNA) sequence. Yet, studies examining cause-effect relationships between environmental stressors, specific epigenetic mechanisms and subsequent responses are still lacking. The present work contributes to increase this knowledge by investigating the effects of Florida Red Tides on two types of mechanisms participating in the epigenetic memory of Eastern oysters: histone variants and DNA methylation. For that purpose, a HAB simulation was conducted in laboratory conditions, exposing oysters to increasing concentrations of K. brevis. The obtained results revealed, for the first time, the existence of H2A.X, H2A.Z and macroH2A genes in this organism, encoding histone variants potentially involved in the maintenance of genome integrity during responses to the genotoxic effect of brevetoxins. Additionally, an increase in H2A.X phosphorylation (γH2A.X, a marker of DNA damage) and a decrease in global DNA methylation were observed as the HAB simulation progressed. Overall, the present work provides a basis to better understand how epigenetic mechanisms participate in responses to environmental stress in marine invertebrates, opening new avenues to incorporate environmental epigenetics approaches into management and conservation programs.
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Affiliation(s)
- Rodrigo Gonzalez-Romero
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Victoria Suarez-Ulloa
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Javier Rodriguez-Casariego
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA; Ecotoxicology and Risk Assessment Laboratory, Southeast Environmental Research Center, Florida International University, North Miami, FL 33181, USA
| | - Daniel Garcia-Souto
- Departamento de Bioquimica, Xenetica e Inmunoloxia, Universidade de Vigo, E-36310 Vigo, Spain
| | - Gabriel Diaz
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Abraham Smith
- Ecotoxicology and Risk Assessment Laboratory, Southeast Environmental Research Center, Florida International University, North Miami, FL 33181, USA
| | - Juan Jose Pasantes
- Departamento de Bioquimica, Xenetica e Inmunoloxia, Universidade de Vigo, E-36310 Vigo, Spain
| | - Gary Rand
- Ecotoxicology and Risk Assessment Laboratory, Southeast Environmental Research Center, Florida International University, North Miami, FL 33181, USA
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA.
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Geyer KK, Niazi UH, Duval D, Cosseau C, Tomlinson C, Chalmers IW, Swain MT, Cutress DJ, Bickham-Wright U, Munshi SE, Grunau C, Yoshino TP, Hoffmann KF. The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005246. [PMID: 28510608 PMCID: PMC5433704 DOI: 10.1371/journal.pntd.0005246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions. Firstly, methyl-CpG binding domain protein (Bgmbd2/3) and DNA methyltransferase 1 (Bgdnmt1) genes are transcriptionally enriched in gonadal compared to somatic tissues with 5-azacytidine (5-AzaC) treatment significantly inhibiting oviposition. Secondly, elevated levels of 5-methyl cytosine (5mC), DNA methyltransferase activity and 5mC binding in pigmented hybrid- compared to inbred (NMRI)- B. glabrata populations indicate a role for the snail's DNA methylation machinery in maintaining hybrid vigour or heterosis. Thirdly, locus-specific detection of 5mC by bisulfite (BS)-PCR revealed 5mC within an exonic region of a housekeeping protein-coding gene (Bg14-3-3), supporting previous in silico predictions and whole genome BS-Seq analysis of this species' genome. Finally, we provide preliminary evidence for parasite-mediated host epigenetic reprogramming in the schistosome/snail system, as demonstrated by the increase in Bgdnmt1 and Bgmbd2/3 transcript abundance following Bge (B. glabrata embryonic cell line) exposure to parasite larval transformation products (LTP). CONCLUSIONS/SIGNIFICANCE The presence of a functional DNA methylation machinery in B. glabrata as well as the modulation of these gene products in response to schistosome products, suggests a vital role for DNA methylation during snail development/oviposition and parasite interactions. Further deciphering the role of this epigenetic process during Biomphalaria/Schistosoma co-evolutionary biology may reveal key factors associated with disease transmission and, moreover, enable the discovery of novel lifecycle intervention strategies.
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Affiliation(s)
- Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Umar H. Niazi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David Duval
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Céline Cosseau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Chad Tomlinson
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David J. Cutress
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Utibe Bickham-Wright
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Sabrina E. Munshi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Christoph Grunau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
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28
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Epigenetic signatures of invasive status in populations of marine invertebrates. Sci Rep 2017; 7:42193. [PMID: 28205577 PMCID: PMC5311950 DOI: 10.1038/srep42193] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/06/2017] [Indexed: 12/27/2022] Open
Abstract
Epigenetics, as a DNA signature that affects gene expression and enables rapid reaction of an organism to environmental changes, is likely involved in the process of biological invasions. DNA methylation is an epigenetic mechanism common to plants and animals for regulating gene expression. In this study we show, for the first time in any marine species, significant reduction of global methylation levels during the expansive phase of a pygmy mussel (Xenostrobus securis) recent invasion in Europe (two-year old), while in older introductions such epigenetic signature of invasion was progressively reduced. Decreased methylation was interpreted as a rapid way of increasing phenotypic plasticity that would help invasive populations to thrive. This epigenetic signature of early invasion was stronger than the expected environmental signature of environmental stress in younger populations sampled from ports, otherwise detected in a much older population (>90 year old) of the also invasive tubeworm Ficopomatus enigmaticus established in similar locations. Higher epigenetic than genetic diversity found in X. securis was confirmed from F. enigmaticus samples. As reported for introduced plants and vertebrates, epigenetic variation could compensate for relatively lower genetic variation caused by founder effects. These phenomena were compared with epigenetic mechanisms involved in metastasis, as parallel processes of community (biological invasion) and organism (cancer) invasions.
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Rivera-Casas C, González-Romero R, Vizoso-Vazquez Á, Cheema MS, Cerdán ME, Méndez J, Ausió J, Eirin-Lopez JM. Characterization of mussel H2A.Z.2: a new H2A.Z variant preferentially expressed in germinal tissues from Mytilus. Biochem Cell Biol 2016; 94:480-490. [DOI: 10.1139/bcb-2016-0056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is especially interesting because of its regulatory role and its differentiation into 2 functionally divergent variants (H2A.Z.1 and H2A.Z.2), further specializing the structure and function of vertebrate chromatin. In the present work we describe, for the first time, the presence of a second H2A.Z variant (H2A.Z.2) in the genome of a non-vertebrate animal, the mussel Mytilus. The molecular and evolutionary characterization of mussel H2A.Z.1 and H2A.Z.2 histones is consistent with their functional specialization, supported on sequence divergence at promoter and coding regions as well as on varying gene expression patterns. More precisely, the expression of H2A.Z.2 transcripts in gonadal tissue and its potential upregulation in response to genotoxic stress might be mirroring the specialization of this variant in DNA repair. Overall, the findings presented in this work complement recent reports describing the widespread presence of other histone variants across eukaryotes, supporting an ancestral origin and conserved role for histone variants in chromatin.
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Affiliation(s)
- Ciro Rivera-Casas
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Rodrigo González-Romero
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Ángel Vizoso-Vazquez
- Exprela Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Manjinder S. Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - M. Esperanza Cerdán
- Exprela Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Josefina Méndez
- Xenomar Group, Department of Cellular and Molecular Biology, University of A Coruña, A Coruña E15071, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Jose M. Eirin-Lopez
- Chromatin Structure and Evolution (Chromevol) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
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30
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Dimond JL, Roberts SB. Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change. Mol Ecol 2016; 25:1895-904. [DOI: 10.1111/mec.13414] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/26/2015] [Accepted: 10/01/2015] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
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31
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Jiang Q, Li Q, Yu H, Kong L. Inheritance and Variation of Genomic DNA Methylation in Diploid and Triploid Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:124-132. [PMID: 26585587 DOI: 10.1007/s10126-015-9674-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
DNA methylation is an important epigenetic mechanism that could be responsive to environmental changes indicating a potential role in natural selection and adaption. In order to evaluate an evolutionary role of DNA methylation, it is essential to first gain a better insight into inheritability. To address this question, this study investigated DNA methylation variation from parents to offspring in the Pacific oyster Crassostrea gigas using fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP) analysis. Most of parental methylated loci were stably transmitted to offspring segregating following Medelian expectation. However, methylated loci deviated more often than non-methylated loci and offspring showed a few de novo methylated loci indicating DNA methylation changes from parents to offspring. Interestingly, some male-specific methylated loci were found in this study which might help to explore sex determination in oyster. Despite environmental stimuli, genomic stresses such as polyploidization also can induce methylation changes. This study also compared global DNA methylation level and individual methylated loci between diploid and triploid oysters. Results showed no difference in global methylation state but a few ploidy-specific loci were detected. DNA methylation variation during polyploidization was less than autonomous methylation variation from parents to offspring.
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Affiliation(s)
- Qun Jiang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Hong Yu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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Dabe EC, Sanford RS, Kohn AB, Bobkova Y, Moroz LL. DNA Methylation in Basal Metazoans: Insights from Ctenophores. Integr Comp Biol 2015; 55:1096-110. [PMID: 26173712 PMCID: PMC4817592 DOI: 10.1093/icb/icv086] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Epigenetic modifications control gene expression without altering the primary DNA sequence. However, little is known about DNA methylation in invertebrates and its evolution. Here, we characterize two types of genomic DNA methylation in ctenophores, 5-methyl cytosine (5-mC) and the unconventional form of methylation 6-methyl adenine (6-mA). Using both bisulfite sequencing and an ELISA-based colorimetric assay, we experimentally confirmed the presence of 5-mC DNA methylation in ctenophores. In contrast to other invertebrates studied, Mnemiopsis leidyi has lower levels of genome-wide 5-mC methylation, but higher levels of 5-mC methylation in promoters when compared with gene bodies. Phylogenetic analysis showed that ctenophores have distinct forms of DNA methyltransferase 1 (DNMT1); the zf-CXXC domain type, which localized DNMT1 to CpG sites, and is a metazoan specific innovation. We also show that ctenophores encode the full repertoire of putative enzymes for 6-mA DNA methylation, and these genes are expressed in the aboral organ of Mnemiopsis. Using an ELISA-based colorimetric assay, we experimentally confirmed the presence of 6-mA methylation in the genomes of three different species of ctenophores, M. leidyi, Beroe abyssicola, and Pleurobrachia bachei. The functional role of this novel epigenomic mark is currently unknown. In summary, despite their compact genomes, there is a wide variety of epigenomic mechanisms employed by basal metazoans that provide novel insights into the evolutionary origins of biological novelties.
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Affiliation(s)
- Emily C Dabe
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rachel S Sanford
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrea B Kohn
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
| | - Yelena Bobkova
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
| | - Leonid L Moroz
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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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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Nikapitiya C, McDowell IC, Villamil L, Muñoz P, Sohn S, Gomez-Chiarri M. Identification of potential general markers of disease resistance in American oysters, Crassostrea virginica through gene expression studies. FISH & SHELLFISH IMMUNOLOGY 2014; 41:27-36. [PMID: 24973516 DOI: 10.1016/j.fsi.2014.06.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Several diseases have a significant impact on American oyster populations in the Atlantic coasts of North America. Knowledge about the responses of oysters to pathogenic challenge could help in identifying potential markers of disease resistance and biomarkers of the health status of an oyster population. A previous analysis of the transcriptome of resistant and susceptible American oysters in response to challenge with the bacterial pathogen Roseovarius crassostreae, as well as sequencing of suppression subtractive hybridization libraries from oysters challenged with the protozoan parasite Perkinsus marinus, provided a list of genes potentially involved in disease resistance or susceptibility. We investigated the patterns of inducible gene expression of several of these genes in response to experimental challenge with the oyster pathogens R. crassostreae, Vibrio tubiashii, and P. marinus. Oysters showing differential susceptibility to R. crassostreae demonstrated differential patterns of expression of genes coding for immune (serine protease inhibitor-1, SPI1) and stress-related (heat shock protein 70, HSP70; arginine kinase) proteins 30 days after challenge with this bacterial pathogen. Differential patterns of expression of immune (spi1, galectin and a matrix metalloproteinase) and stress-related (hsp70, histone H4, and arginine kinase) genes was observed in hemocytes from adult oysters challenged with P. marinus, but not with V. tubiashii. While levels of spi1 expression in hemocytes collected 8 and 21 days after P. marinus challenge were negatively correlated with parasite load in oysters tissues at the end of the challenge (62 days), levels of expression of hsp70 in hemocytes collected 1-day after challenge were positively correlated with oyster parasite load at 62 days. Our results confirm previous research on the role of serine protease inhibitor-1 in immunity and disease resistance in oysters. They also suggest that HSP70 and histone H4 could be used as a markers of health status or disease susceptibility in oysters.
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Affiliation(s)
- Chamilani Nikapitiya
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, CBLS169, Kingston, RI 02881, USA
| | - Ian C McDowell
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, CBLS169, Kingston, RI 02881, USA
| | - Luisa Villamil
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, CBLS169, Kingston, RI 02881, USA
| | - Pilar Muñoz
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, CBLS169, Kingston, RI 02881, USA
| | - SaeBom Sohn
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, CBLS169, Kingston, RI 02881, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, CBLS169, Kingston, RI 02881, USA.
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Olson CE, Roberts SB. Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes. Front Physiol 2014; 5:224. [PMID: 24987376 PMCID: PMC4060414 DOI: 10.3389/fphys.2014.00224] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 01/21/2023] Open
Abstract
DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity.
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Affiliation(s)
- Claire E Olson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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Rivière G. Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates. Front Physiol 2014; 5:129. [PMID: 24778620 PMCID: PMC3985014 DOI: 10.3389/fphys.2014.00129] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/14/2014] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is evolutionarily conserved. Vertebrates exhibit high, widespread DNA methylation whereas invertebrate genomes are less methylated, predominantly within gene bodies. DNA methylation in invertebrates is associated with transcription level, alternative splicing, and genome evolution, but functional outcomes of DNA methylation remain poorly described in lophotrochozoans. Recent genome-wide approaches improve understanding in distant taxa such as molluscs, where the phylogenetic position, and life traits of Crassostrea gigas make this bivalve an ideal model to study the physiological and evolutionary implications of DNA methylation. We review the literature about DNA methylation in invertebrates and focus on DNA methylation features in the oyster. Indeed, though our MeDIP-seq results confirm predominant intragenic methylation, the profiles depend on the oyster's developmental and reproductive stage. We discuss the perspective that oyster DNA methylation could be biased toward the 5'-end of some genes, depending on physiological status, suggesting important functional outcomes of putative promoter methylation from cell differentiation during early development to sustained adaptation of the species to the environment.
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Affiliation(s)
- Guillaume Rivière
- Institute for Fundamental and Applied Biology, Normandy UniversityCaen, France
- UMR BOREA ‘Biologie des Organismes et Ecosystèmes Aquatiques’ Université de Caen Basse-Normandie, MNHN, UPMC, CNRS-7208, IRD-207Caen, France
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