short read sequencing and shellfish
DESCRIPTION
PAGXX Presentation 2012TRANSCRIPT
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Steven RobertsUniversity of WashingtonSchool of Aquatic and Fishery Sciences
Short-read sequencing used for genomic characterization in aquacultured shellfish
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Traits
disease resistance
stress tolerance
disease resistance
growth
color
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Traits
disease resistance
growth
color
Tran
scrip
tom
e
disease resistance
stress tolerance
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Traits
disease resistance
growth
color
Epigenetics
disease resistance
m
m
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Outline
Disease tolerance [Mercenaria mercenaria]
Environmental response [Ruditapes philippinarum]
Epigenenetics [Crassostrea gigas]
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Disease toleranceQPX and Mercenaria mercenaria
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Disease tolerance
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Disease tolerance
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Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
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Ken Hammond
1 year
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
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Ken Hammond
12% QPX Prevalence
45% QPX Prevalence
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
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Ken Hammond
100 million reads
8482 contigs
RNA-Seq
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100 million reads
8482 contigs
RNA-Seq
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100 million reads
8482 contigs
RNA-Seq
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Ken Hammond
684 DEGs
459 higher in BARN (superior)
RNA-Seq
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684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
RNA-Seq
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Ken Hammond
684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
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Ken Hammond
684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
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684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
apoptosis baculoviral IAP repeat-containing protein, apoptosis 1 inhibitor, TNF receptor-associated factor 3, protein FADDadhesion neuroglian, protocadherin oxidation reduction processes peroxidasin, thyroid peroxidase, epidermis-type lipoxygenase, hydroxysteroid 11-beta-dehydrogenase, carbonyl reductase, cytochrome P450, superoxide dismutase, sorbitol dehydrogenasetranslation asparaginyl-tRNA synthetase, eukaryotic initiation factor, tryptophanyl-tRNA synthetase, eukaryotic peptide chain release factor subunit
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Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Genotyping
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Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Reduce Representation
Genotyping
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Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Reduce Representation
Genotyping
Sequence multiple individuals
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Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Reduce Representation
Genotyping
Sequence multiple individuals
145 Diagnostic Markers
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Environmental stressOcean acidification and clam larvaeRuditapes philippinarum
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Environmental stressOcean acidification and clam larvaeRuditapes philippinarum
Locales in PNW already experiencing acidified conditions
Above Figure: Alin et al.Feely et al. 2008, 2010
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Larval Exposures:No affect on growth or survival
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
240 million reads
RNA-Seq
3800 : 162 DEGs781 annotated55 processes
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
240 million reads
RNA-Seq
3800 : 162 DEGs781 annotated55 processes
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Translation
ATP coupled proton transport
Development
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Translation
ATP coupled proton transport
Development
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Translation
ATP coupled proton transport
Development
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Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Larval Exposures:No affect on growth or survival
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EpigeneticsDNA methylation in Crassostrea gigas
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EpigeneticsDNA methylation in Crassostrea gigas
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EpigeneticsDNA methylation in Crassostrea gigas
www.tokresource.org
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EpigeneticsMBD-Seq
genomic DNA
fragmentY
Y
Y
MBD
MBD
MBD enrich
sequence
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EpigeneticsMBD-Seq
Roberts and Gavery 2012
in silico analysis
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Roberts and Gavery 2012
Epigenetics - directions
Are epigenetic marks independent of genetics marks?
What role do epigenetic marks play in commercially important traits?
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Epigenetics - directions
Are epigenetic marks independent of genetics marks?
High resolution mapping effortsCoupling Bisulfite Sequencing with MBD
What role do epigenetic marks play in commercially important traits?
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SummaryLimited, ultra-short read sequencing can efficiently provide relevant biological information and genomic resources.
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SummaryLimited, ultra-short read sequencing can efficiently provide relevant biological information and genomic resources.
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SummaryLimited, ultra-short read sequencing can efficiently provide relevant biological information and genomic resources.
Availability of shared transcriptomic and genomic sequences will facilitate increased application of short-read sequencing technology to improve aquaculture production.
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Acknowledgementsfunding
USDANRAC
NOAA Saltonstall-Kennedy Washington Sea Grant
Scott LindellDave BushekJohn KraeuterCaroline Storer
Carolyn FriedmanDave MetzgerPaul McElhaneyShallin BuschSam White
Mackenzie Gavery
more information
EPASTAR
UW
goo.gl/TJgA2
fish.washington.edu/genefish
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