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
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Phylotastic metagenomics
- 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 community Community analysis VERY Difficult! EASY High-throughput sequencing
- 6. Explicitly Phylogenetic Approaches Aligned Evolutionary environmental Placement of sequences short reads Guide Tree
- 8. Tree Reconciliation in PhyloSift Environmental Named Sequences Taxa
- 9. 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
- 10. 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
- 11. Integrating Comparative Data • Metadata is a standard part of any well- constructed metagenomics study – Depth (marine samples) – Aquatic/Terrestrial – Temperature – pH – Dissolved Oxygen
- 12. 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
- 13. 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
- 14. Exploring Trees Ecologically, wh at are these reference taxa doing??
- 15. Pertinent info for biological interpretations of DNA data!!
Notes de l'éditeur
- 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?