PAGXX Presentation 2012

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

8. Disease tolerance

9. Disease tolerance

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