nsa2012 short reads and oyster genome resources
DESCRIPTION
Presentation given at NSA 2012 (Seattle, WA)TRANSCRIPT
Steven RobertsUniversity of WashingtonSchool of Aquatic and Fishery Sciences
Short-read sequencing used for genomic characterization in aquacultured shellfish
Traits
disease resistance
stress tolerance
disease resistance
growth
color
Traits
disease resistance
growth
color
Tran
scrip
tom
e
disease resistance
stress tolerance
Traits
disease resistance
growth
color
Epigenetics
disease resistance
m
m
Outline
Disease tolerance [Mercenaria mercenaria]
Environmental response [Ostrea lurida]
Epigenenetics [Crassostrea gigas]
Disease toleranceQPX and Mercenaria mercenaria
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Ken Hammond
1 year
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Ken Hammond
12% QPX Prevalence
45% QPX Prevalence
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Ken Hammond
100 million reads
8482 contigs
RNA-Seq
Ken Hammond
684 DEGs
459 higher in BARN (superior)
RNA-Seq
684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
RNA-Seq
Ken Hammond
684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
Ken Hammond
684 DEGs
459 higher in BARN (superior)
33 enriched biological processes
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
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Genotyping
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Reduce Representation
Genotyping
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Reduce Representation
Genotyping
Sequence multiple individuals
Broodstock :survived disease
pressure
Broodstock :naive to disease
pressure
BARN MASH
Restriction EnzymeAssistedDigestion-Sequencing
Reduce Representation
Genotyping
Sequence multiple individuals
145 Diagnostic Markers
Environmental stressOcean acidification and oyster larvaeOstrea lurida
Environmental stress
400 million reads
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
Environmental stress
400 million reads
RNA-Seq
9605 DEGs7474 annotated4345 processes
55 enriched processes
de novo assembly
Ocean acidification and oyster larvaeOstrea lurida
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.
EpigeneticsDNA methylation in Crassostrea gigas
EpigeneticsDNA methylation in Crassostrea gigas
EpigeneticsDNA methylation in Crassostrea gigas
www.tokresource.org
EpigeneticsMBD-Seq
genomic DNA
fragmentY
Y
Y
MBD
MBD
MBD enrich
sequence
Epigenetics
Y Y
Y
MBD
MBD
MBD
High resolution mapping effortsCoupling Bisulfite Sequencing with MBD
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?
Genomic Resourcesfor Crassostrea gigas
Essential for epigenetic analysis and valuable for other efforts.
Genomic Resourcesfor Crassostrea gigas
Genomic Resourcesfor Crassostrea gigas
Tracks
Genomic Resourcesfor Crassostrea gigas
Tracks (files) can be viewed in a variety of software.
most are free
Genomic Resourcesfor Crassostrea gigas
Developing simple portal(JBrowse)
Genomic Resourcesfor Crassostrea gigas
Galaxy - is an open, web-based platform for data intensive
biomedical research.
Genomic Resourcesfor Crassostrea gigas
•Methylation•alternative splicing•mutation•transient methylation•relationship with gene expression
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
SummaryLimited, ultra-short read sequencing can efficiently provide relevant biological information and genomic resources.
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.
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
