Short-read sequencing used forgenomic characterization inaquacultured shellfishSteven RobertsUniversity of WashingtonSchoo...
e                             growth    disease resistance            color                               stress          ...
e                                    growth           disease resistance            color                                 ...
e                               growth    disease resistance              color                    Traits     m    m      ...
Outline     Disease tolerance [Mercenaria mercenaria]Environmental response [Ruditapes philippinarum]                Epige...
Disease toleranceQPX and Mercenaria mercenaria
Disease tolerance
Disease tolerance
Broodstock :       Broodstock :survived disease   naive to disease    pressure           pressure   BARN              MASH
Broodstock :                Broodstock :survived disease            naive to disease    pressure                    pressu...
Broodstock :                Broodstock :survived disease            naive to disease    pressure                    pressu...
RNA-Seq                    Ken Hammond100 million reads  8482 contigs
RNA-Seq100 million reads  8482 contigs
RNA-Seq100 million reads  8482 contigs
RNA-Seq                  Ken Hammond  684 DEGs 459 higher inBARN (superior)
RNA-Seq  684 DEGs 459 higher inBARN (superior) 33 enriched  biological  processes
Ken Hammond  684 DEGs 459 higher inBARN (superior) 33 enriched  biological  processes
Ken Hammond  684 DEGs 459 higher inBARN (superior) 33 enriched  biological  processes
apoptosis                  baculoviral IAP repeat-containing protein,                  apoptosis 1 inhibitor, TNF receptor...
Broodstock :       Broodstock :Genotyping           survived disease                         pressure                     ...
Broodstock :       Broodstock :Genotyping           survived disease                         pressure                     ...
Broodstock :       Broodstock :Genotyping            survived disease                          pressure                   ...
Broodstock :       Broodstock :Genotyping            survived disease                          pressure                   ...
Environmental stressOcean acidification and clam larvaeRuditapes philippinarum
Environmental stressOcean acidification and clam larvaeRuditapes philippinarum                    Locales in PNW already  ...
Environmental stressOcean acidification and clam larvae                        Larval Exposures:                        No...
Environmental stressOcean acidification and clam larvae                            240 million reads                      ...
Environmental stressOcean acidification and clam larvae                            240 million reads                      ...
Environmental stressOcean acidification and clam larvae                            Translation                            ...
Environmental stressOcean acidification and clam larvae                            Translation                            ...
Environmental stressOcean acidification and clam larvae                            Translation                            ...
Environmental stressOcean acidification and clam larvae   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  fragment                           MBD                           Y            ...
EpigeneticsMBD-Seq              in silico analysis                                   Roberts and Gavery 2012
Epigenetics - directions   Are epigenetic marks independent of   genetics marks?   What role do epigenetic marks play in  ...
Epigenetics - directions   Are epigenetic marks independent of   genetics marks?   What role do epigenetic marks play in  ...
SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.
SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.
SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.Av...
AcknowledgementsScott Lindell                 fundingDave Bushek        USDAJohn Kraeuter      NRACCaroline Storer    NOAA...
Short read sequencing and shellfish
Short read sequencing and shellfish
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Short read sequencing and shellfish

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Short read sequencing and shellfish

  1. 1. Short-read sequencing used forgenomic characterization inaquacultured shellfishSteven RobertsUniversity of WashingtonSchool of Aquatic and Fishery Sciences
  2. 2. e growth disease resistance color stress tolerance Traits
  3. 3. e growth disease resistance color stress tolerance e Traits m to rip c nsTra
  4. 4. e growth disease resistance color Traits m m Epigenetics
  5. 5. Outline Disease tolerance [Mercenaria mercenaria]Environmental response [Ruditapes philippinarum] Epigenenetics [Crassostrea gigas]
  6. 6. Disease toleranceQPX and Mercenaria mercenaria
  7. 7. Disease tolerance
  8. 8. Disease tolerance
  9. 9. Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH
  10. 10. Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH 1 year Ken Hammond
  11. 11. Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH 12% QPX Prevalence 45% QPX Prevalence Ken Hammond
  12. 12. RNA-Seq Ken Hammond100 million reads 8482 contigs
  13. 13. RNA-Seq100 million reads 8482 contigs
  14. 14. RNA-Seq100 million reads 8482 contigs
  15. 15. RNA-Seq Ken Hammond 684 DEGs 459 higher inBARN (superior)
  16. 16. RNA-Seq 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes
  17. 17. Ken Hammond 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes
  18. 18. Ken Hammond 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes
  19. 19. apoptosis baculoviral IAP repeat-containing protein, apoptosis 1 inhibitor, TNF receptor- associated factor 3, protein FADD adhesion 684 DEGs neuroglian, protocadherin oxidation reduction processes 459 higher in peroxidasin, thyroid peroxidase, epidermis-type lipoxygenase,BARN (superior) hydroxysteroid 11-beta-dehydrogenase, 33 enriched carbonyl reductase,  cytochrome P450, superoxide dismutase, sorbitol biological dehydrogenase processes translation asparaginyl-tRNA synthetase, eukaryotic initiation factor, tryptophanyl-tRNA synthetase, eukaryotic peptide chain release factor subunit
  20. 20. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction EnzymeAssistedDigestion-Sequencing
  21. 21. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing
  22. 22. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing Sequence multiple individuals
  23. 23. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing Sequence multiple individuals 145 Diagnostic Markers
  24. 24. Environmental stressOcean acidification and clam larvaeRuditapes philippinarum
  25. 25. Environmental stressOcean acidification and clam larvaeRuditapes philippinarum Locales in PNW already experiencing acidified conditions Above Figure: Alin et al. Feely et al. 2008, 2010
  26. 26. Environmental stressOcean acidification and clam larvae Larval Exposures: No affect on growth or survival Metzger et al. in review
  27. 27. Environmental stressOcean acidification and clam larvae 240 million reads RNA-Seq 3800 : 162 DEGs 781 annotated 55 processes Metzger et al. in review
  28. 28. Environmental stressOcean acidification and clam larvae 240 million reads RNA-Seq 3800 : 162 DEGs 781 annotated 55 processes Metzger et al. in review
  29. 29. Environmental stressOcean acidification and clam larvae Translation ATP coupled proton transport Development Metzger et al. in review
  30. 30. Environmental stressOcean acidification and clam larvae Translation ATP coupled proton transport Development Metzger et al. in review
  31. 31. Environmental stressOcean acidification and clam larvae Translation ATP coupled proton transport Development Metzger et al. in review
  32. 32. Environmental stressOcean acidification and clam larvae Larval Exposures: No affect on growth or survival Metzger et al. in review
  33. 33. EpigeneticsDNA methylation in Crassostrea gigas
  34. 34. EpigeneticsDNA methylation in Crassostrea gigas
  35. 35. EpigeneticsDNA methylation in Crassostrea gigas www.tokresource.org
  36. 36. EpigeneticsMBD-Seq genomic DNA fragment MBD Y MBD Y enrich MBD Y sequence
  37. 37. EpigeneticsMBD-Seq in silico analysis Roberts and Gavery 2012
  38. 38. Epigenetics - directions Are epigenetic marks independent of genetics marks? What role do epigenetic marks play in commercially important traits? Roberts and Gavery 2012
  39. 39. Epigenetics - directions Are epigenetic marks independent of genetics marks? What role do epigenetic marks play in commercially important traits? High resolution mapping efforts Coupling Bisulfite Sequencing with MBD
  40. 40. SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.
  41. 41. SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.
  42. 42. SummaryLimited, ultra-short read sequencing canefficiently provide relevant biologicalinformation and genomic resources.Availability of shared transcriptomic andgenomic sequences will facilitate increasedapplication of short-read sequencingtechnology to improve aquacultureproduction.
  43. 43. AcknowledgementsScott Lindell fundingDave Bushek USDAJohn Kraeuter NRACCaroline Storer NOAA Saltonstall-Kennedy Washington Sea GrantCarolyn FriedmanDave Metzger EPA UWPaul McElhaney STARShallin BuschSam White more information fish.washington.edu/genefishMackenzie Gavery goo.gl/TJgA2
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