Phylotastic! Metagenomics Use Cases

Holly Bik, UC Davis

-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

Biodiversity?

Phylogeography?

Environmental Impacts?

Extract Environmental DNA

Amplify rRNA

High-throughput sequencing

Community analysis

Diverse marine community

EASYEASY

EASY

VERY Difficult!

http://phylosift.wordpress.com

Explicitly Phylogenetic ApproachesAligned environmentalsequences

Guide Tree

Evolutionary Placement of short reads

Tree Reconciliation in PhyloSift

Environmental Sequences

Named Taxa

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

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

Integrating Comparative Data

• Metadata is a standard part of any well-constructed metagenomics study

– Depth (marine samples)– Aquatic/Terrestrial– Temperature– pH– Dissolved Oxygen

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

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

Exploring Trees

Ecologically, what are these reference taxa doing??

Pertinent info for biological interpretations of DNA data!!