genetic variation of renibacterium salmoninarum genes jeffrey burnett dr. dan rockey laboratory...
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Genetic Variation of Renibacterium salmoninarum
Genes
Jeffrey BurnettDr. Dan Rockey Laboratory
Biomedical SciencesCollege of Veterinary Medicine
Acknowledgements
• Dr. Dan Rockey• Dr. Katharine G. Field• Dr. Ling Jin• Dr. Damir Alzhanov• Dr. Kevin Ahern• Wanda Crannell• Rockey Lab
– Brendan, Kelsey, Sara
Introduction
Hypothesis
Methods
Results
Conclusion
Acknowledgements
• Dr. Greg Wiens• Whole Genome Sequencing of
Renibacterium salmoninarum – USDA-CREES 2004-35600-14173
• Howard Hughes Medical Institute
Introduction
Hypothesis
Methods
Results
Conclusion
Who should care…
• Anyone who enjoys salmon– fishing / recreation– gastronomy
• Ecosystem Balance• Economics
– Communities depend on salmon for subsistence
Introduction
Hypothesis
Methods
Results
Conclusion
Who should care…
Introduction
Hypothesis
Methods
Results
Conclusion
Smith, Pedro et al. Principales enfermedades de los peces salmonídeos cultivados en chile. Monografías de Medicina Veterinaria, Vol.21(2), diciembre 2001.
R. salmoninarum vs. Arthrobacter spp.
• Arthrobacter spp.– Diverse group of soil-dwelling
microbes– 5.9 Mb genome– Used in bioremediation,
extracellular polysaccharide synthesis
Introduction
Hypothesis
Methods
Results
Conclusion
R. Salmoninarum vs. Arthrobacter spp.
• R. salmoninarum– 3.1 Mb genome– Fastidious– Facultative intracellular pathogen– Farmed and wild salmon species
• Worldwide
– Vertical and horizontal transmission
Introduction
Hypothesis
Methods
Results
Conclusion
Genome Sequencing Project
• R. salmoninarum ATCC33209– Completed in December 2007– Inactivated open reading frames– Supports reductive evolution
hypothesis
Introduction
Hypothesis
Methods
Results
Conclusion
MAUVE output : courtesy Dr. Greg Wiens, NWFSC
Sequencing results
Introduction
Hypothesis
Methods
Results
Conclusion
VS.
Hypothesis
• The highly frameshifted genome sequence of Renibacterium salmoninarum ATCC 33209 is an artifact of extensive culture in vitro.
Introduction
Hypothesis
Methods
Results
Conclusion
Acquired R. salmoninarum samples
• ATCC33209– Chinook Salmon
• Leaburg, Oregon, USA (1974)
• mt239– Atlantic Salmon (Salmo salar), Scotland
• 684– Brown Trout (Salmo Trutta), Norway
• Clinical samples (A and B)– Chinook Salmon (Onchorhyncus tschawytscha)
• Bonneville Fish Hatchery, Oregon
Introduction
Hypothesis
Methods
Results
Conclusion
Genes selected for analysis
Introduction
Hypothesis
Methods
Results
Conclusion
Sequencing results
• dppD/F (F) – 5’ GGC.CGC.GAT.GTG.TCG.ATG.GTT.TT
• dppD/F (R) – 5’ GCC.CAA.GTG.CGG.CAC.TGC.AGC• C. Syn. (F) – 5’ GCG.CGG.AGA.GAA.GTT.CTT.GTG• C. Syn. (R) – 5’ CGA.TGC.GGT.GCG.ACG.TTT.T• tetP (F) – 5’ GCC.TAG.CGA.CGC.AAA.AG• tetP (R) – 5’ ATA.GTG.ACT.AAG.CAA.TCG.GTG• FBP (F) – 5’ CTG.ACG.CCA.ACG.GTA.AAT.ACA.CC• FBP (R) – 5’ GGC.GGA.TTC.TCA.ACA.CTC.ACG
Introduction
Hypothesis
Methods
Results
Conclusion
Chemically competent E.coli cell
X 60 samples
Center for Genome Research and Biocomputing
@ OSU
Results
Introduction
Hypothesis
Methods
Results
Conclusion
tetPtetP dppD/FdppD/F c. sync. syn FBPFBP
AA ++ ++ ++
BB ++ ++ ++ ++
mt239mt239 ++ ++ ++ ++
684684 ++ ++ ++
ATCCATCC ++ ++ ++ ++
Sequencing results
Introduction
Hypothesis
Methods
Results
Conclusion
Sequencing results
Introduction
Hypothesis
Methods
Results
Conclusion
Sequencing results
Introduction
Hypothesis
Methods
Results
Conclusion
Conclusions
• Sequence suggests significant reductive evolution
• Transition to pathogenic lifestyle
• No evidence that the ATCC 33209 strain is irrepresentative of what is found in nature
Introduction
Hypothesis
Methods
Results
Conclusion
Conclusions
• Mutations represented in the sequence genome are not a function of culture in vitro
Introduction
Hypothesis
Methods
Results
Conclusion
Questions?