Short read sequencing and shellfish
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Steven Roberts University of Washington School of Aquatic and Fishery Sciences Short-read sequencing used for genomic characterization in aquacultured shellfish
description
PAGXX Presentation 2012
Transcript of Short read sequencing and shellfish
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 [Ruditapes philippinarum]
Epigenenetics [Crassostrea gigas]
Disease toleranceQPX and Mercenaria mercenaria
Disease tolerance
Disease tolerance
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
100 million reads
8482 contigs
RNA-Seq
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 clam larvaeRuditapes philippinarum
Environmental stressOcean acidification and clam larvaeRuditapes philippinarum
Locales in PNW already experiencing acidified conditions
Above Figure: Alin et al.Feely et al. 2008, 2010
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Larval Exposures:No affect on growth or survival
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
240 million reads
RNA-Seq
3800 : 162 DEGs781 annotated55 processes
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
240 million reads
RNA-Seq
3800 : 162 DEGs781 annotated55 processes
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Translation
ATP coupled proton transport
Development
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Translation
ATP coupled proton transport
Development
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Translation
ATP coupled proton transport
Development
Environmental stressOcean acidification and clam larvae
Metzger et al. in review
Larval Exposures:No affect on growth or survival
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
EpigeneticsMBD-Seq
Roberts and Gavery 2012
in silico analysis
Roberts and Gavery 2012
Epigenetics - directions
Are epigenetic marks independent of genetics marks?
What role do epigenetic marks play in commercially important traits?
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?
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.
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.
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
