Phylotastic metagenomics

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Examples of metagenomics use cases for the Phylotastic! web tools. Presented a the Phylotastic hackathon, June 4-8 2012: http://www.evoio.org/wiki/Phylotastic

Examples of metagenomics use cases for the Phylotastic! web tools. Presented a the Phylotastic hackathon, June 4-8 2012: http://www.evoio.org/wiki/Phylotastic

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  • You can ignore all the other bad –Omic words you hear – conservome?!
  • Regardless of methdology, focus on:Species assemblages and taxonomic diversityCommunity patterns over space and time – Cosmoplitanism or Regionally restricted?Community changes as a result of natural/human disturbance
  • Marker genes across all domains – bacteria, archeaa,eukaryotes & virusesrRNA genes,Protein-coding orthologs, lineage-specific gene families----- Meeting Notes (5/22/12 10:42) -----Marker genes to make higher level taxon assignmentsLineages-specific gene families to narrow down assignments to lower taxonomic levels
  • Head-tail patterns may help us to delimit species and separate out rare taxa (who will have Head-tail patterns) from errors (no apparent pattern)----- Meeting Notes (5/22/12 10:42) -----pplacer and EPA are great tools developed in the last few years.
  • I see name matching as not just species names, but matching between NCBI taxon ID synonyms
  • rRNAdata especially needs to be interpreted in a phylogenetic contextPhylo placement allows:1) More robust taxon assignments2) ID divergent/undersampled lineages (that aren't apparent via BLAST searches)What's the ecology/function of these divergent lineages?

Transcript

  • 1. Phylotastic!Metagenomics Use Cases Holly Bik, UC Davis
  • 2. -Omic Dictionary• Marker gene studies – amplification of a conserved homologous gene (18S, 16S rRNA) from environmental samples• Metagenomics – shotgun sequencing of random genomic fragments from environmental DNA
  • 3. Biodiversity? Phylogeography? Environmental Impacts?
  • 4. Extract Environmental DNA EASY EASY Amplify rRNA Diverse marine communityCommunity analysis VERY Difficult! EASY High-throughput sequencing
  • 5. http://phylosift.wordpress.com
  • 6. Explicitly Phylogenetic Approaches Aligned Evolutionary environmental Placement of sequences short reads Guide Tree
  • 7. Tree Reconciliation in PhyloSift Environmental Named Sequences Taxa
  • 8. Pruning Subtrees from Megatrees• User inputs a list of reference sequences with NCBI Taxon IDs  Pulls down tree topology• Unclassified sequences in a reference phylogeny could be “named” with the most appropriate higher level taxon
  • 9. Name Matching and TNRS• Different taxonomic synonyms have different NCBI taxon IDS – Shigella: 620 and E.coli: 562 – Species/genus boundaries still debated• TNRS would provide a “matrix” for standardizing IDs – E.g. E.coli/Shigella supergroup: 12345
  • 10. Integrating Comparative Data• Metadata is a standard part of any well- constructed metagenomics study – Depth (marine samples) – Aquatic/Terrestrial – Temperature – pH – Dissolved Oxygen
  • 11. Integrating Comparative Data• Metadata also includes information about the sequences themselves – Abundance information – Distribution across sample sites Branch thickness can be incorporated into XML tree files and visualized within Archaeopteryx
  • 12. Mashup with Online Data• Pull down NCBI metadata for a given reference sequence accession – Habitat metadata – Ecological associations –e.g. symbionts – Genome availability – Related publications – Pictures, etc. would be awesome
  • 13. Exploring Trees Ecologically, wh at are these reference taxa doing??
  • 14. Pertinent info for biologicalinterpretations of DNA data!!