nsa2012 short reads and oyster genome resources
DESCRIPTION
Presentation given at NSA 2012 (Seattle, WA)TRANSCRIPT
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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 [Ostrea lurida]
Epigenenetics [Crassostrea gigas]
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Disease toleranceQPX and Mercenaria mercenaria
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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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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 oyster larvaeOstrea lurida
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Environmental stress
400 million reads
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
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Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
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Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
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Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
![Page 26: NSA2012 Short reads and Oyster Genome Resources](https://reader034.vdocument.in/reader034/viewer/2022042623/5485c55c5806b5c2588b47ae/html5/thumbnails/26.jpg)
Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
![Page 27: NSA2012 Short reads and Oyster Genome Resources](https://reader034.vdocument.in/reader034/viewer/2022042623/5485c55c5806b5c2588b47ae/html5/thumbnails/27.jpg)
Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
Can provide informationon physiological impact that
might not be directly evident.
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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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Epigenetics
Y Y
Y
MBD
MBD
MBD
High resolution mapping effortsCoupling Bisulfite Sequencing with MBD
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Epigenetics - directions
Are epigenetic marks independent of genetics marks?
What role do epigenetic marks play in commercially important traits?
What are the mechanisms of action of DNA methylation marks?
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Genomic Resourcesfor Crassostrea gigas
Essential for epigenetic analysis and valuable for other efforts.
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Genomic Resourcesfor Crassostrea gigas
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Genomic Resourcesfor Crassostrea gigas
Tracks
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Genomic Resourcesfor Crassostrea gigas
Tracks (files) can be viewed in a variety of software.
most are free
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Genomic Resourcesfor Crassostrea gigas
Developing simple portal(JBrowse)
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Genomic Resourcesfor Crassostrea gigas
Galaxy - is an open, web-based platform for data intensive
biomedical research.
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Genomic Resourcesfor Crassostrea gigas
•Methylation•alternative splicing•mutation•transient methylation•relationship with gene expression
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Genomic Resourcesfor Crassostrea gigas
•Gene Discovery
•qPCR design
•RNA-Seq
•RAD-Seq
•Gene Structure
•Genetic Diversity
•Phylogenetics
•more...
•Methylation•alternative splicing•mutation•transient methylation•relationship with gene expression
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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.
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Acknowledgementsfunding
USDANRAC
NOAA Saltonstall-Kennedy Washington Sea Grant
Scott LindellDave BushekJohn KraeuterCaroline Storer
Carolyn FriedmanDave MetzgerSam White
Mackenzie Gaverymore information
EPASTAR
UW
fish.washington.edu/genefish
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