The Wolbachia genome revealed an unexpectedly high amount of repetitive DNA and mobile genetic elements (which were never seen before in a small-genomed intracellular species)
Jonathan Eisen talk on "Enodsymbiont Genomics" at Lake Arrowhead Small Genomes Meeting 2006
NO TITLEJonathan A. Eisen U. C. Davis
Famous Arrowhead Quotes 2006• Publications, student degrees, etc.• Not trying to say anything bad about anyone• The human guts are a real milieu• Where’s you evening gown?• You better kiss everybody• This is how you do metagenomics on 50 dollars, and that’s Canadian dollars
Lessons Learned at Arrowhead 2006• Open availability of genome sequences has revolutionized microbiology• Open Source software tools can help allow non informatics specialists to make use of genome data• Open genome databases can make sense of disparate information
Lessons Not Yet Learned• What about Open Access to publications?• Open Access can revolutionize the use of the literature just as Genbank revolutionized the use of sequence data
Outline• Introduction• Three endosymbiont genomics tales – Wolbachia – Sharpshooter – Calyptogena• Where next?
Sources for the Origin of Novelty• New biochemical functions – Evolution of new genes – Old genes with new functions – Mixing and matching existing genes• Changes in uses of existing genes – Targeting – Regulation• Acquisition of new functions – Recombination – Lateral gene transfer – Symbioses
Endosymbioses Drove Eukaryotic Evolution QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture.
But ….• Key questions unresolved – Was the pre-organelle ancestor free-living? – What the ancestor a mutualist? a parasite? – What happened early in the evolution of the symbiosis?• The problems with organelles – Symbioses were so long ago that it is nearly impossible to figure out what the early events were. – May represent frozen accidents• Solution? – Study more recent and more diverse symbioses
Wolbachia pipientis wMel• Wolbachia are obligate, maternally transmitted intracellular symbionts• Wolbachia infect many invertebrate species – Many cause male specific deleterious effects – Model system for studying sex ratio changes in hosts – Some are mutualistic (e.g., in filarial nematodes)• wMel selected as model system because it infects Drosophila melanogaster
Wolbachia Metagenomic Sequencing QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. shotgun QuickTime™ and aTIFF (Uncompressed) decompressor are needed to see this picture. sequence QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Analysis led by Matin Wu in collaboration with lab of Scott O’Neill
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Endosymbiont Trends• Compared to free-living relatives – Smaller genomes – Lower GC content – Higher pIs – Higher rates of sequence evolution• Wolbachia shows ALL of these – However ….
Explanations for EndosymbiontDifferences with Free-Living Relatives• Repair hypothesis – Loss of DNA repair genes leads to increased mutation rate – Trends are the direct and indirect result of this increased mutation rate• Population genetics hypothesis – Smaller effective population size leads to more genetic drift – Trends are mostly the result of accumulation of slightly deleterious mutations• PopGen explanations favored – Wolbachia has full suite of repair genes
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Glassy Winged Sharpshooter Symbiont • Vector for Pierce’s disease in grapes • Potential bioterror agent • Feeds on nutrient poor xylem sap • Needs to get amino- acids and other nutrients from symbionts like aphids Wu et al. PLoS Biology 2006
Explanations for Endosymbiont Differences with Each Other• Repair hypothesis• Population genetics hypothesis• Repair explanations favored
Polymorphisms in Metapopulation• Data from ~200 hosts – 104 SNPs – 2 indels• PCR surveys show that this is between host variation• Much lower ratio of transitions:transversions than in Blochmannia• Consistent with absence of MMR from Blochmannia
Metagenomics, Symbionts and Binning • Understanding multisymbiont ecosystems is greatly aided by binning • Multiple methods can be QuickTime™ and a TIFF (LZW) decompressorare needed to see this picture. combined for better signal – Assembly – Composition – Phylogeny – Depth of coverage
Binning in More Complex Systems?A TB UC VD WE XF YG Z
C. magnifica symbiont sequencing• Collaboration between Cavanaugh Lab at Harvard (Irene Newton led analysis), Eisen lab, and JGI (Woyke and others).• Funded by DOE through CSP program and sequencing and closure done at JGI• Annotation and analysis involved DOE (JGI, ORNL), Harvard, TIGR, Davis, et al.
What is Next II+?• Vertical vs. environmental transmission – Two chemosymbioses – P.I. C. M. Cavanaugh, Harvard• Chordate symbionts – Prochloron - tunicate – P.I. Jacques Ravel, TIGR.• Epibionts – AMH epibiont of Alvinella worm – P.I. Craig Cary. U. Delaware• Commensals
TIGR $$$ N. Ward C. Fraser J. Heidelberg Frase Other people DOE E. Eisenstadt Moore NSF N. Moran S. Salzberg NIH H. Ochman VI F. Robb I. Paulsen J. Venter M. WuJ. Battista R. Myers D. RuschE. Orias D. Wu A. HalpernD. Bryant M. Frazier S. Chatterji S. O’Neill M. Eisen H. Huse P. Hanawalt E. Rubin C. M. Cavanaugh T. Woyke A. Hartman J. Morgan JGI Eisen Mom and Dad Group
Correlation of Endosymbiont Features • Correlation makes it difficult to tease apart cause and effect • Need examples where properties are decoupled • May be the case in Baumannia with genome size
Long Term Effects of Repair Loss• Endosymbionts are model systems for understanding the consequences of loss of repair activities• RecA lost in Buchnera and Blochmannia but kept in Baumannia and Wigglesworthia• MutSL loss mentioned previously• RecBCD present even in species without RecA• Mfd present in many species without UvrABCD
Famous Arrowhead 2004 Quotes• Space-time continuum of genes and genomes• Gene sequences are the wormhole that allows one to tunnel into the past• The human mind can conceive of things with no basis in physical reality• Thoughts can go faster than the speed of light