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Short read sequencing and shellfish
- 1. Short-read sequencing used for genomic characterization in aquacultured shellfish Steven Roberts University of Washington School of Aquatic and Fishery Sciences
- 3. e growth disease resistance color stress tolerance Traits
- 4. e growth disease resistance color stress tolerance e Traits m to rip c ns Tra
- 5. e growth disease resistance color Traits m m Epigenetics
- 6. Outline Disease tolerance [Mercenaria mercenaria] Environmental response [Ruditapes philippinarum] Epigenenetics [Crassostrea gigas]
- 7. Disease tolerance QPX and Mercenaria mercenaria
- 10. Broodstock : Broodstock : survived disease naive to disease pressure pressure BARN MASH
- 11. Broodstock : Broodstock : survived disease naive to disease pressure pressure BARN MASH 1 year Ken Hammond
- 12. Broodstock : Broodstock : survived disease naive to disease pressure pressure BARN MASH 12% QPX Prevalence 45% QPX Prevalence Ken Hammond
- 13. RNA-Seq Ken Hammond 100 million reads 8482 contigs
- 14. RNA-Seq 100 million reads 8482 contigs
- 15. RNA-Seq 100 million reads 8482 contigs
- 16. RNA-Seq Ken Hammond 684 DEGs 459 higher in BARN (superior)
- 17. RNA-Seq 684 DEGs 459 higher in BARN (superior) 33 enriched biological processes
- 18. Ken Hammond 684 DEGs 459 higher in BARN (superior) 33 enriched biological processes
- 19. Ken Hammond 684 DEGs 459 higher in BARN (superior) 33 enriched biological processes
- 20. 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
- 21. Broodstock : Broodstock : Genotyping survived disease pressure naive to disease pressure BARN MASH Restriction Enzyme Assisted Digestion - Sequencing
- 22. Broodstock : Broodstock : Genotyping survived disease pressure naive to disease pressure BARN MASH Restriction Enzyme Reduce Representation Assisted Digestion - Sequencing
- 23. Broodstock : Broodstock : Genotyping survived disease pressure naive to disease pressure BARN MASH Restriction Enzyme Reduce Representation Assisted Digestion - Sequencing Sequence multiple individuals
- 24. Broodstock : Broodstock : Genotyping survived disease pressure naive to disease pressure BARN MASH Restriction Enzyme Reduce Representation Assisted Digestion - Sequencing Sequence multiple individuals 145 Diagnostic Markers
- 25. Environmental stress Ocean acidification and clam larvae Ruditapes philippinarum
- 26. Environmental stress Ocean acidification and clam larvae Ruditapes philippinarum Locales in PNW already experiencing acidified conditions Above Figure: Alin et al. Feely et al. 2008, 2010
- 27. Environmental stress Ocean acidification and clam larvae Larval Exposures: No affect on growth or survival Metzger et al. in review
- 28. Environmental stress Ocean acidification and clam larvae 240 million reads RNA-Seq 3800 : 162 DEGs 781 annotated 55 processes Metzger et al. in review
- 29. Environmental stress Ocean acidification and clam larvae 240 million reads RNA-Seq 3800 : 162 DEGs 781 annotated 55 processes Metzger et al. in review
- 30. Environmental stress Ocean acidification and clam larvae Translation ATP coupled proton transport Development Metzger et al. in review
- 31. Environmental stress Ocean acidification and clam larvae Translation ATP coupled proton transport Development Metzger et al. in review
- 32. Environmental stress Ocean acidification and clam larvae Translation ATP coupled proton transport Development Metzger et al. in review
- 33. Environmental stress Ocean acidification and clam larvae Larval Exposures: No affect on growth or survival Metzger et al. in review
- 34. Epigenetics DNA methylation in Crassostrea gigas
- 35. Epigenetics DNA methylation in Crassostrea gigas
- 36. Epigenetics DNA methylation in Crassostrea gigas www.tokresource.org
- 37. Epigenetics MBD-Seq genomic DNA fragment MBD Y MBD Y enrich MBD Y sequence
- 38. Epigenetics MBD-Seq in silico analysis Roberts and Gavery 2012
- 39. Epigenetics - directions Are epigenetic marks independent of genetics marks? What role do epigenetic marks play in commercially important traits? Roberts and Gavery 2012
- 40. 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
- 41. Summary Limited, ultra-short read sequencing can efficiently provide relevant biological information and genomic resources.
- 42. Summary Limited, ultra-short read sequencing can efficiently provide relevant biological information and genomic resources.
- 43. Summary Limited, 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.
- 44. Acknowledgements Scott Lindell funding Dave Bushek USDA John Kraeuter NRAC Caroline Storer NOAA Saltonstall-Kennedy Washington Sea Grant Carolyn Friedman Dave Metzger EPA UW Paul McElhaney STAR Shallin Busch Sam White more information fish.washington.edu/genefish Mackenzie Gavery goo.gl/TJgA2