Neufeld ISME14

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Targeted recovery of novel phylogenetic diversity from next-generation sequence data

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Neufeld ISME14

  1. 1. Targeted recovery of novel phylogenetic diversity from next-generation sequence data Josh D. NeufeldUNIVERSITY OFWATERLOO
  2. 2. 1. Value of studying rare tax 2. Targeted exploration of phylogenetic noveltyUNIVERSITY OFWATERLOO
  3. 3. Carlos Pedrós-Alió (2012)
  4. 4. Why study rare microbial taxa?Estimate the total number of taxa in samplesAnswer whether “everything is everywhere.”Test ecological mechanisms for subsistenceIdentify genes with novel applications Reveal phylogenetic novelty, undetected due to previous methodological limitations Carlos Pedrós-Alió (2012) Josh Neufeld
  5. 5. HypothesisRare 16S rRNA genesequences arephylogeneticallynovel and representpersistent low abundancepopulations.
  6. 6. Next-gen sequence dataPotentially novel clades16S rRNA gene phylogeny
  7. 7. Michael Lynch Poster 023A Thursday
  8. 8. 1. Value of studying rare taxa 2. Targeted exploration of phylogenetic novelty
  9. 9. Alert, Nunavut82°28 N, 62°30 WNeufeld et al. 2005
  10. 10. Bartram et al. 2011
  11. 11. PhylumClassOrder
  12. 12. SILVASSU-Parc 106
  13. 13. SILVASSU-Parc 106
  14. 14. ssu-alignRDP training set
  15. 15. PCRcloningSanger
  16. 16. Genbankcultured uncultured Lynch et al. 2012
  17. 17. SILVALiving Tree Project
  18. 18. Nakai et al. 2012SILVALiving Tree Project Lynch et al. 2012
  19. 19. UL9Lynch et al. 2012
  20. 20. Rare taxa representphylogenetic noveltySSUnique and networkanalysis help filter dataAdded value for largedatasets
  21. 21. Thank you@JoshDNeufeldjneufeld@uwaterloo.ca

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