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NSA2012 Short reads and Oyster Genome Resources

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Presentation given at NSA 2012 (Seattle, WA)

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NSA2012 Short reads and Oyster Genome Resources

  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 [Ostrea lurida] Epigenenetics [Crassostrea gigas]
  6. 6. Disease toleranceQPX and Mercenaria mercenaria
  7. 7. Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH
  8. 8. Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH 1 year Ken Hammond
  9. 9. Broodstock : Broodstock :survived disease naive to disease pressure pressure BARN MASH 12% QPX Prevalence 45% QPX Prevalence Ken Hammond
  10. 10. RNA-Seq Ken Hammond100 million reads 8482 contigs
  11. 11. RNA-Seq Ken Hammond 684 DEGs 459 higher inBARN (superior)
  12. 12. RNA-Seq 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes
  13. 13. Ken Hammond 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes
  14. 14. Ken Hammond 684 DEGs 459 higher inBARN (superior) 33 enriched biological processes
  15. 15. 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
  16. 16. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction EnzymeAssistedDigestion-Sequencing
  17. 17. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing
  18. 18. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing Sequence multiple individuals
  19. 19. Broodstock : Broodstock :Genotyping survived disease pressure naive to disease pressure BARN MASHRestriction Enzyme Reduce RepresentationAssistedDigestion-Sequencing Sequence multiple individuals 145 Diagnostic Markers
  20. 20. Environmental stressOcean acidification and oyster larvaeOstrea lurida
  21. 21. Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly
  22. 22. Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq 9605 DEGs 7474 annotated 4345 processes
  23. 23. Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq 9605 DEGs 7474 annotated 4345 processes 55 enriched processes
  24. 24. Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq 9605 DEGs 7474 annotated 4345 processes 55 enriched processes
  25. 25. Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq 9605 DEGs 7474 annotated 4345 processes 55 enriched processes
  26. 26. Environmental stressOcean acidification and oyster larvaeOstrea lurida 400 million reads de novo assembly RNA-Seq Can provide information on physiological impact that 9605 DEGs might not be directly evident. 7474 annotated 4345 processes 55 enriched processes
  27. 27. EpigeneticsDNA methylation in Crassostrea gigas
  28. 28. EpigeneticsDNA methylation in Crassostrea gigas
  29. 29. EpigeneticsDNA methylation in Crassostrea gigas www.tokresource.org
  30. 30. EpigeneticsMBD-Seq genomic DNA fragment MBD Y MBD Y enrich MBD Y sequence
  31. 31. Epigenetics High resolution mapping efforts Coupling Bisulfite Sequencing with MBD MBD Y MBD Y MBD Y
  32. 32. 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?
  33. 33. Genomic Resourcesfor Crassostrea gigas Essential for epigenetic analysis and valuable for other efforts.
  34. 34. Genomic Resourcesfor Crassostrea gigas
  35. 35. Genomic Resourcesfor Crassostrea gigas Tracks
  36. 36. Genomic Resourcesfor Crassostrea gigas Tracks (files) can be viewed in a variety of software. most are free
  37. 37. Genomic Resourcesfor Crassostrea gigas Developing simple portal (JBrowse)
  38. 38. Genomic Resourcesfor Crassostrea gigas Galaxy - is an open, web-based platform for data intensive biomedical research.
  39. 39. Genomic Resourcesfor Crassostrea gigas •Methylation •alternative splicing •mutation •transient methylation •relationship with gene expression
  40. 40. Genomic Resourcesfor Crassostrea gigas •Gene Discovery •Methylation •qPCR design •alternative •RNA-Seq splicing •mutation •RAD-Seq •transient •Gene Structure methylation •Genetic Diversity •relationship with gene expression •Phylogenetics •more...
  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.
  43. 43. Acknowledgements fundingScott Lindell USDADave Bushek NRACJohn KraeuterCaroline Storer NOAA Saltonstall-Kennedy Washington Sea GrantCarolyn Friedman EPA UWDave Metzger STARSam White more informationMackenzie Gavery fish.washington.edu/genefish

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