Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes.

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Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes.

Front Physiol. 2014;5:224

Authors: Olson CE, Roberts SB

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.

PMID: 24987376 [PubMed]

via pubmed: school of aquatic an… http://ift.tt/1vMZfYb

Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon.

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Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon.

Biogerontology. 2013 Oct;14(5):483-90

Authors: Storer CS, Quinn TP, Roberts SB

Abstract
Senescence varies considerably among fishes, and understanding the evolutionary basis for this diversity has become an important area of study. For rapidly senescing species such as Pacific salmon, senescence is a complex process as these fish are initiating anorexia while migrating to natal spawning grounds, and die within days of reproduction. To better understand senescence in Pacific salmon we examined expression patterns for a suite of genes in brain tissue of pre-senescent and senescent sockeye salmon. Interestingly, a significant increase in expression of genes involved in telomere repair and immune activity was observed in senescent salmon. These data provide insight into physiological changes in salmon undergoing senescence and the factors contributing to variation in observed senescence rates among individuals and populations.

PMID: 23948798 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://ift.tt/1oZN8Fd

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc.

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Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc.

PeerJ. 2013;1:e215

Authors: Gavery MR, Roberts SB

Abstract
Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.

PMID: 24282674 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/24282674?dopt=Abstract

Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon.

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Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon.

Biogerontology. 2013 Aug 15;

Authors: Storer CS, Quinn TP, Roberts SB

Abstract
Senescence varies considerably among fishes, and understanding the evolutionary basis for this diversity has become an important area of study. For rapidly senescing species such as Pacific salmon, senescence is a complex process as these fish are initiating anorexia while migrating to natal spawning grounds, and die within days of reproduction. To better understand senescence in Pacific salmon we examined expression patterns for a suite of genes in brain tissue of pre-senescent and senescent sockeye salmon. Interestingly, a significant increase in expression of genes involved in telomere repair and immune activity was observed in senescent salmon. These data provide insight into physiological changes in salmon undergoing senescence and the factors contributing to variation in observed senescence rates among individuals and populations.

PMID: 23948798 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23948798?dopt=Abstract

Genomic resource development for shellfish of conservation concern.

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Genomic resource development for shellfish of conservation concern.

Mol Ecol Resour. 2013 Mar;13(2):295-305

Authors: Timmins-Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB

Abstract
Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species.

PMID: 23280275 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23280275?dopt=Abstract

Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

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Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

PLoS One. 2012;7(11):e49018

Authors: Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE

Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.

PMID: 23185290 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23185290?dopt=Abstract

Genomic resource development for shellfish of conservation concern.

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Genomic resource development for shellfish of conservation concern.

Mol Ecol Resour. 2012 Dec 27;

Authors: Timmins-Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB

Abstract
Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species.

PMID: 23280275 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23280275?dopt=Abstract

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

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Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

PLoS One. 2012;7(11):e49018

Authors: Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE

Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.

PMID: 23185290 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23185290?dopt=Abstract

Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

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Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

Comp Biochem Physiol Part D Genomics Proteomics. 2012 Jun;7(2):94-9

Authors: Gavery MR, Roberts SB

Abstract
Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genomes. However, there are limited examples that rely solely on ultra-short read sequencing technologies (e.g. Solexa, SOLiD) for transcript discovery and gene expression analysis (i.e. RNA-Seq). Here we use SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes. Gene enrichment analysis determined that in addition to biological processes predicted to be associated with anthropogenic influences (e.g. immune response), other processes play important roles including cell recognition and cell adhesion. To evaluate the effectiveness of restricting characterization solely to short read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold. This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms.

PMID: 22244882 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/22244882?dopt=Abstract