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Ximing Guo - One of the best experts on this subject based on the ideXlab platform.
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development of snp panels as a new tool to assess the genetic diversity population structure and parentage analysis of the Eastern Oyster crassostrea virginica
Marine Biotechnology, 2018Co-Authors: Wilawan Thongda, Ximing Guo, Sean P Powers, Honggang Zhao, Dongdong Zhang, Lauren N Jescovitch, Ming Liu, Meagan N Schrandt, Eric PeatmanAbstract:Culture of the Eastern Oyster (Crassostrea virginica) is rapidly expanding. Combined with their continuing role as an environmental sentinel species and ecological model, this trend necessitates improved molecular tools for breeding and selection, as well as population assessment and genetic conservation. Here, we describe the development and validation of two panels of 58 single nucleotide polymorphism markers (SNPs) for the species. Population analyses revealed three distinct populations, based on FST values and STRUCTURE, among wild Oysters sampled from Delaware Bay (1), northwest Florida (2), Alabama (2), Louisiana (2), and the Texas Gulf Coast (3), consistent with previous microsatellite and mtDNA analyses. In addition, utilizing the developed panels for parentage assignment in cultured Oysters (Rutgers, New Jersey) resulted in a highly accurate identification of parent pairs (99.37%). The SNP markers could, furthermore, clearly discriminate between hatchery stocks and wild-sourced individuals. The developed SNP panels may serve as an important tool for more rapid and affordable genetic analyses in Eastern Oyster.
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production of inbred larvae through self fertilization using oocytes and cryopreserved sperm from the same individuals after sex reversal in Eastern Oyster crassostrea virginica
Aquaculture Research, 2015Co-Authors: Huiping Yang, Ximing Guo, Yan Wang, Terrence R TierschAbstract:The Eastern Oyster Crassostrea virginica can change sex which makes self-fertilization possible if sperm can be cryopreserved. In this study, small (~1 year old) and large (~2–3 years old) Oysters were biopsied for sperm collection. Survival of the biopsied Oysters after 1 year was 50% for small Oysters and 17% for large Oysters. Oocytes were collected from sex-reversed females, and self-fertilized with cryopreserved sperm. Of the 24 cryopreserved samples, 14 individuals had ≤1% fertility when crossed with oocytes from unrelated females, indicating that the cryopreserved sperm had reduced fertility. The other 10 individuals had a fertility of 39 ± 25% when crossed with oocytes from unrelated females (non-selfing), but showed a significantly lower success of self-fertilization (12 ± 16%) (P = 0.008), while aliquots of the same oocytes had a fertilization of 83 ± 11% when crossing with fresh sperm. Larvae were produced at day 3 in the self-fertilized families (12–94% of the fertilized oocytes), and survived to eyed-larvae stage at days 11–14. Genotyping with 9 microsatellite markers confirmed that the larvae resulted from self-fertilization in four families. This study demonstrated the feasibility of creating self-fertilized inbred lines of Oysters by use of non-lethal sperm collection and cryopreservation.
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developing tools for the study of molluscan immunity the sequencing of the genome of the Eastern Oyster crassostrea virginica
Fish & Shellfish Immunology, 2015Co-Authors: Marta Gomezchiarri, Ximing Guo, Wesley C Warren, Dina A. ProestouAbstract:The Eastern Oyster, Crassostrea virginica, provides important ecological and economical services, making it the target of restoration projects and supporting a significant fishery/aquaculture industry with landings valued at more than $100 million in 2012 in the United States of America. Due to the impact of infectious diseases on wild, restored, and cultured populations, the Eastern Oyster has been the focus of studies on host-pathogen interactions and immunity, as well as the target of selective breeding efforts for disease resistant Oyster lines. Despite these efforts, relatively little is known about the genetic basis of resistance to diseases or environmental stress, not only in Eastern Oyster, but also in other molluscan species of commercial interest worldwide. In order to develop tools and resources to assist in the elucidation of the genomic basis of traits of commercial, biological, and ecological interest in Oysters, a team of genome and bioinformatics experts, in collaboration with the Oyster research community, is sequencing, assembling, and annotating the first reference genome for the Eastern Oyster and producing an exhaustive transcriptome from a variety of Oyster developmental stages and tissues in response to a diverse set of environmentally-relevant stimuli. These transcriptomes and reference genome for the Eastern Oyster, added to the already available genome and transcriptomes for the Pacific Oyster (Crassostrea gigas) and other bivalve species, will be an essential resource for the discovery of candidate genes and markers associated with traits of commercial, biological, and ecologic importance in bivalve molluscs, including those related to host-pathogen interactions and immunity.
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transcriptome analysis reveals a rich gene set related to innate immunity in the Eastern Oyster crassostrea virginica
Marine Biotechnology, 2014Co-Authors: Linlin Zhang, Yabing Zhu, Guofan Zhang, Ximing GuoAbstract:As a benthic filter-feeder of estuaries, the Eastern Oyster, Crassostrea virginica, faces tremendous exposure to microbial pathogens. How Eastern Oysters without adaptive immunity survive in pathogen-rich environments is of fundamental interest, but studies on its immune system are hindered by the lack of genomic resources. We sequenced the transcriptome of an adult Oyster with short Illumina reads and assembled 66,229 contigs with a N50 length of 1,503 bp. The assembly covered 89.4 % of published ESTs and 97.9 % of mitochondrial genes demonstrating its quality. A set of 39,978 contigs and unigenes (>300 bp) were identified and annotated by searching public databases. Analysis of the gene set yielded a diverse set of 657 genes related to innate immunity, including many pertaining to pattern recognition, effectors, signal transduction, cytokines, and apoptosis. Gene families encoding C1q domain containing proteins, CTLD, IAPs, Ig_I-set, and TRAFs expanded in C. virginica and Crassostrea gigas. Many key genes of the apoptosis system including IAP, BAX, BAC-2, caspase, FADD, and TNFR were identified, suggesting C. virginica posses advanced apoptosis and apoptosis-regulating systems. Our results show that short Illumina reads can produce transcriptomes of highly polymorphic genomes with coverage and integrity comparable to that from longer 454 reads. The expansion and high diversity in gene families related to innate immunity, point to a complex defense system in the lophotrochozoan C. virginica, probably in adaptation to a pathogen-rich environment.
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nonlethal sperm collection and cryopreservation in the Eastern Oyster crassostrea virginica
Journal of Shellfish Research, 2013Co-Authors: Huiping Yang, Ximing Guo, John Supan, Terrence R TierschAbstract:Cryopreservation can preserve genetic materials in perpetuity and can be applied to Oyster culture for breeding programs. Protocols exist for sperm cryopreservation in the Eastern Oyster Crassostrea virginica, but nonlethal sample collection is needed for valuable individuals, such as tetraploids, or specific lines. The goal of this study was to develop nonlethal methods for sperm collection in the Eastern Oyster. The objectives were (1) to evaluate natural spawning as a collection method, (2) to evaluate anesthesia methods to induce shell opening for biopsy, (3) to evaluate mechanical notching for biopsy, and (4) to verify notching combined with biopsy for collection and cryopreservation. Five males (of 60 Oysters) spawned naturally after 7 h, with an average sperm concentration of 1.9 ± 1.0310 3 cells/mL (in 2 L seawater). No Oysters (n ¼ 30) responded by opening during 36 h of treatment with 5% Dead Sea salt (containing 33.3% MgCl2), and 22 Oysters (of 30) opened during the 36-h treatment with 5% Epson salt (MgSO4). Sperm collected by biopsy had fresh motility of 3%-80% and postthaw motility of 1%-5%; sperm production was 4.53 10 5 to 2.3310 8 cells per male. Mechanical notching did not cause mortality to Oysters (n ¼ 20). After notching and biopsy with 18-G and 20-G needles, survival was 80% (16 of 20 for each). Sperm production was 5.42 3 10 7 cells by 18-G needle (n ¼ 8) with fresh motility of 16± 12% and postthaw motility of 3± 2%, and 1.35310 8 cells by 20-G needle (n ¼ 9) with fresh motility of 21± 20% and postthaw motility of 5 ± 4%. No differences were observed between samples biopsied with the 2 needle sizes (P $ 0.074). To verify notching and biopsy for nonlethal sperm collection, a total of 39 Oysters were sampled to obtain 20 males, which averaged 99.48 ± 23.17 g total weight, 74.1 ± 6.0 mm shell height, and 60.9 ± 7.2 mm shell length. The sperm production was 3.6 ± 2.1 3 10 8 cells per male. Biopsied sperm showed 23 ± 12% fresh motility, 13 ± 6% postequilibration motility (after equilibration with 10% of DMSO for 30-60 min before freezing), and 6± 4% postthaw motility. Flow cytometry analysis indicated an average of 84± 4% of cells with intact plasma membranes for fresh sperm, and 59± 9% for postthaw sperm. Fertilization by thawed sperm averaged 20± 22% (from 1%-87%). No significant differences were observed between the biopsied samples and the dissected samples (lethal collection) for fresh motility (P ¼ 0.550), postequilibration motility (P ¼ 1.000), postthaw motility (P ¼ 0.101), fresh membrane integrity (P ¼ 1.000), or postthaw membrane integrity (P ¼ 1.000), but a difference was observed in fertilization (P ¼ 0.039; biopsied samples, 20± 22%; dissected samples, 68 ± 40%). Overall, this study developed notching combined with biopsy for sperm collection and cryopreservation in Eastern Oysters that can be applied to valuable individuals and breeding programs.
Sigrun Lange - One of the best experts on this subject based on the ideXlab platform.
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Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca-The Blue Mussel (Mytilus edulis), Soft Shell Clam (Mya arenaria), Eastern Oyster (Crassostrea virginica) and Atlantic Jacknife Clam (Ensis leei).
Biology, 2020Co-Authors: Timothy J. Bowden, Igor Kraev, Sigrun LangeAbstract:Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern Oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern Oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.
Timothy J. Bowden - One of the best experts on this subject based on the ideXlab platform.
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Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca-The Blue Mussel (Mytilus edulis), Soft Shell Clam (Mya arenaria), Eastern Oyster (Crassostrea virginica) and Atlantic Jacknife Clam (Ensis leei).
Biology, 2020Co-Authors: Timothy J. Bowden, Igor Kraev, Sigrun LangeAbstract:Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern Oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern Oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.
Morgan W Kelly - One of the best experts on this subject based on the ideXlab platform.
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evolutionary change in the Eastern Oyster crassostrea virginica following low salinity exposure
Integrative and Comparative Biology, 2021Co-Authors: Joanna S Griffiths, Kevin M Johnson, Morgan W KellyAbstract:The presence of standing genetic variation will play a role in determining a population's capacity to adapt to environmentally relevant stressors. In the Gulf of Mexico, extreme climatic events and anthropogenic changes to local hydrology will expose productive Oyster breeding grounds to stressful low salinity conditions. We identified genetic variation for performance under low salinity (due to the combined effects of low salinity and genetic load) using a single-generation selection experiment on larvae from two populations of the Eastern Oyster, Crassostrea virginica. We used pool-sequencing to test for allele frequency differences at 152 salinity-associated genes for larval families pre- and post-low salinity exposure. Our results have implications for how evolutionary change occurs during early life history stages at environmentally relevant salinities. Consistent with observations of high genetic load observed in Oysters, we demonstrate evidence for purging of deleterious alleles at the larval stage in C. virginica. In addition, we observe increases in allele frequencies at multiple loci, suggesting that natural selection for low salinity performance at the larval stage can act as a filter for genotypes found in adult populations.
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transcriptomic signatures of temperature adaptation in the Eastern Oyster crassostrea virginica
Journal of Evolutionary Biology, 2021Co-Authors: Jerome F La Peyre, Sandra M Casas, Kevin M Johnson, Hollis R Jones, Morgan W KellyAbstract:The large geographic distribution of the Eastern Oyster, Crassostrea virginica, makes it an ideal species to test how populations have adapted to latitudinal gradients in temperature. Despite inhabiting distinct thermal regimes, populations of C. virginica near the species' southern and northern geographic range show no population differences in their physiological response to temperature. In this study, we used comparative transcriptomics to understand how Oysters from either end of the species' range maintain enantiostasis across three acclimation temperatures (10, 20, and 30°C). With this approach, we identified genes that were differentially expressed in response to temperature between individuals of C. virginica collected from New Brunswick, Canada and Louisiana, USA. We observed a core set of genes whose expression responded to temperature in both populations, but also an even larger set of genes with expression patterns that were unique to each population. Intriguingly, the genes with population-specific responses to temperature had elevated FST and Ka/Ks ratios compared to the genome-wide average. In contrast, genes showing only a response to temperature were found to only have elevated FST values suggesting that divergent FST may be due to selection on linked regulatory regions rather than positive selection on protein coding regions. Taken together, our results suggest that, despite coarse-scale physiological similarities, natural selection has shaped divergent gene expression responses to temperature in geographically separated populations of this broadly eurythermal marine invertebrate.
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characterizing the epigenetic and transcriptomic responses to perkinsus marinus infection in the Eastern Oyster crassostrea virginica
Frontiers in Marine Science, 2020Co-Authors: Kevin M Johnson, Jerome F La Peyre, Sandra M Casas, K A Sirovy, Morgan W KellyAbstract:Eastern Oyster populations in the northern Gulf of Mexico are routinely infected with the protistan parasite Perkinsus marinus, the cause of the disease commonly known as dermo. Recent experimental challenges among Atlantic coast populations have identified both resistant and susceptible genotypes using comparative transcriptomics. While controlled experimental challenges are essential first assessments, expanding this analysis to field reared individuals provides an opportunity to identify key genomic signatures of infection that appear both in the laboratory and in the field. In this study we combined reduced representation bisulfite sequencing with 3’ RNA sequencing (Tag-seq) to describe two molecular phenotypes associated with infection in Oysters outplanted at a common garden field site. These combined approaches allowed us to examine changes in DNA methylation and gene expression for a large number of individuals (n=40) that developed infections during the course of a common garden outplant experiment. Our epigenetic analysis of DNA methylation identified significant changes in gene body methylation associated with increasing infection intensity, across genes associated with immune responses. There was a smaller transcriptomic response to increasing infection intensities with 32 genes showing differential expression, and 40 % of these genes were found to also be differentially methylated. While there was no clear pattern between direction of differential methylation and gene expression, there was a significant effect of percent methylation on gene-by-gene expression levels and the coefficient of variation in gene body methylation between treatments. These results show that heavily methylated genes have high levels of gene expression with low levels of variation. Comparing our differential expression results with previously published experimental P. marinus challenges identified overlapping expression patterns for genes associated with C1q-domain-containing and V-type proton ATPase proteins. Through our comparative transcriptomic approach using field reared individuals and co-expression network analysis we have also been able to identify a network of genes that change in expression in response to infection. These combined analyses provide evidence for a conserved response to P. marinus infections and suggest that gene body DNA methylation is a better predictor of gene expression variation than it is of the overall magnitude of gene expression.
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population epigenetic divergence exceeds genetic divergence in the Eastern Oyster crassostrea virginica in the northern gulf of mexico
Evolutionary Applications, 2020Co-Authors: Kevin M Johnson, Morgan W KellyAbstract:Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome-wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern Oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site-associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene-wide averages of FST, and DNA methylation differences between Oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low FST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore Oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in FST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population-specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene-body mean FST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.
Kevin M Johnson - One of the best experts on this subject based on the ideXlab platform.
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evolutionary change in the Eastern Oyster crassostrea virginica following low salinity exposure
Integrative and Comparative Biology, 2021Co-Authors: Joanna S Griffiths, Kevin M Johnson, Morgan W KellyAbstract:The presence of standing genetic variation will play a role in determining a population's capacity to adapt to environmentally relevant stressors. In the Gulf of Mexico, extreme climatic events and anthropogenic changes to local hydrology will expose productive Oyster breeding grounds to stressful low salinity conditions. We identified genetic variation for performance under low salinity (due to the combined effects of low salinity and genetic load) using a single-generation selection experiment on larvae from two populations of the Eastern Oyster, Crassostrea virginica. We used pool-sequencing to test for allele frequency differences at 152 salinity-associated genes for larval families pre- and post-low salinity exposure. Our results have implications for how evolutionary change occurs during early life history stages at environmentally relevant salinities. Consistent with observations of high genetic load observed in Oysters, we demonstrate evidence for purging of deleterious alleles at the larval stage in C. virginica. In addition, we observe increases in allele frequencies at multiple loci, suggesting that natural selection for low salinity performance at the larval stage can act as a filter for genotypes found in adult populations.
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transcriptomic signatures of temperature adaptation in the Eastern Oyster crassostrea virginica
Journal of Evolutionary Biology, 2021Co-Authors: Jerome F La Peyre, Sandra M Casas, Kevin M Johnson, Hollis R Jones, Morgan W KellyAbstract:The large geographic distribution of the Eastern Oyster, Crassostrea virginica, makes it an ideal species to test how populations have adapted to latitudinal gradients in temperature. Despite inhabiting distinct thermal regimes, populations of C. virginica near the species' southern and northern geographic range show no population differences in their physiological response to temperature. In this study, we used comparative transcriptomics to understand how Oysters from either end of the species' range maintain enantiostasis across three acclimation temperatures (10, 20, and 30°C). With this approach, we identified genes that were differentially expressed in response to temperature between individuals of C. virginica collected from New Brunswick, Canada and Louisiana, USA. We observed a core set of genes whose expression responded to temperature in both populations, but also an even larger set of genes with expression patterns that were unique to each population. Intriguingly, the genes with population-specific responses to temperature had elevated FST and Ka/Ks ratios compared to the genome-wide average. In contrast, genes showing only a response to temperature were found to only have elevated FST values suggesting that divergent FST may be due to selection on linked regulatory regions rather than positive selection on protein coding regions. Taken together, our results suggest that, despite coarse-scale physiological similarities, natural selection has shaped divergent gene expression responses to temperature in geographically separated populations of this broadly eurythermal marine invertebrate.
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characterizing the epigenetic and transcriptomic responses to perkinsus marinus infection in the Eastern Oyster crassostrea virginica
Frontiers in Marine Science, 2020Co-Authors: Kevin M Johnson, Jerome F La Peyre, Sandra M Casas, K A Sirovy, Morgan W KellyAbstract:Eastern Oyster populations in the northern Gulf of Mexico are routinely infected with the protistan parasite Perkinsus marinus, the cause of the disease commonly known as dermo. Recent experimental challenges among Atlantic coast populations have identified both resistant and susceptible genotypes using comparative transcriptomics. While controlled experimental challenges are essential first assessments, expanding this analysis to field reared individuals provides an opportunity to identify key genomic signatures of infection that appear both in the laboratory and in the field. In this study we combined reduced representation bisulfite sequencing with 3’ RNA sequencing (Tag-seq) to describe two molecular phenotypes associated with infection in Oysters outplanted at a common garden field site. These combined approaches allowed us to examine changes in DNA methylation and gene expression for a large number of individuals (n=40) that developed infections during the course of a common garden outplant experiment. Our epigenetic analysis of DNA methylation identified significant changes in gene body methylation associated with increasing infection intensity, across genes associated with immune responses. There was a smaller transcriptomic response to increasing infection intensities with 32 genes showing differential expression, and 40 % of these genes were found to also be differentially methylated. While there was no clear pattern between direction of differential methylation and gene expression, there was a significant effect of percent methylation on gene-by-gene expression levels and the coefficient of variation in gene body methylation between treatments. These results show that heavily methylated genes have high levels of gene expression with low levels of variation. Comparing our differential expression results with previously published experimental P. marinus challenges identified overlapping expression patterns for genes associated with C1q-domain-containing and V-type proton ATPase proteins. Through our comparative transcriptomic approach using field reared individuals and co-expression network analysis we have also been able to identify a network of genes that change in expression in response to infection. These combined analyses provide evidence for a conserved response to P. marinus infections and suggest that gene body DNA methylation is a better predictor of gene expression variation than it is of the overall magnitude of gene expression.
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population epigenetic divergence exceeds genetic divergence in the Eastern Oyster crassostrea virginica in the northern gulf of mexico
Evolutionary Applications, 2020Co-Authors: Kevin M Johnson, Morgan W KellyAbstract:Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome-wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern Oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site-associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene-wide averages of FST, and DNA methylation differences between Oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low FST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore Oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in FST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population-specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene-body mean FST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.