• GEBA

• A genomic encyclopedia of bacteria and archaea

Eisen & Ward, PIs

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

Firmicutes

Fusobacteria

Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

• Genome sequences are mostly from three phyla

• Some other phyla are only sparsely sampled

• Solution: Really Fill in the Tree

GEBA Pilot Project Overview

• Identify major branches in rRNA tree for which no genomes are available

• Identify those with a cultured representative in DSMZ

• DSMZ grew > 200 of these and prepped DNA

• Sequence and finish 100+ (covering breadth of bacterial/archaea diversity)

• Annotate, analyze, release data• Assess benefits of tree guided

sequencing• 1st paper Wu et al in Nature Dec

2009

* The rRNA Tree of Life is a Useful Tool for Identifying Phylogenetically Novel Genomes

* Phylogeny-driven genome selection helps discover new genetic diversity

* Phylogeny driven genome selection (and phylogenetics in general) improves genome annotation

* Improves analysis of genome data from uncultured organisms (not by too much)

GEBA Phylogenomic Lessons

Organism Selection Method I

MaxPD : Select organisms so the phylogentic diversity is maximized on a 16S rRNA tree

CLUSTER_56 number of sequences=3 genome representatives=0(10934,10867,237295)

Desulfobotulus sp. str. BG14Desulfocella halophila str. GSL-But2 DSMZ:DSM11763 TYPE STRAINDesulfocella sp. str. DSM 2056 DSMZ:DSM2056

CLUSTER_57 number of sequences=3 genome representatives=1(10775,10774,71864)

Desulfoarculus sp. str. BG74Desulfovibrio baarsii str. 2st14Desulfovibrio baarsii str. DSM 2075 DSMZ:DSM2075 Gi03014 TYPE STRAIN

MCL Clustering: divide organisms in a phylogenetic group in subgroups

Organism Selection Method II