Prokaryotic vs. eukaryotic genomes

Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233.

Genome organization in bacteria

Published by AAAS

P. Glaser et al., Science 294, 849-852 (2001)

Comparison of two Listeria genomes

• Food-borne pathogen• Meningitis

Phe 12s rRNAVal

16s rRNA

LeuIle

Gln

Met

Trp

Ala

Asn

Cys

Tyr

COI

SerAspCOII

LysATP8

ATP6COIII

GlyNADH3

Arg

NADH4L

NADH4

His

Ser

Leu

NADH5

Cyt b

Thr

Control Region

Pro

NADH6

Glu

noncoding

What is this?

rRNA genes

tRNA genes

ATP synthase genes

Cytochrome bc1 complex

Cytochrome Oxidase

NADH:Ubiquinone Oxidoreductase

NADH1

NADH2

The Rickettsia genome - ancestor of mitochondrial DNA

Plasmids and microbial evolutionVibrio cholerae genome

19.10 Phylogenetic evidence for lateral gene transfer from Archaea to Entamoeba histolytica

Genomic turnover and HGT in the -Proteobacteria

Gene expansion in microbes over time

Genome stasis in Buchnera

Buchnera and ancestral enteric bacteria (E. coli)Gray areas area ancestral genomic components lost

Copyright ©2005 by the National Academy of Sciences

Ochman, Howard (2005) Proc. Natl. Acad. Sci. USA 102, 11959-11960

Fig. 1. Relationships of sequenced bacterial genomes showing that in both the {alpha}- and {gamma}-proteobacteria, lineages with smaller genome sizes are derived from ancestors that had larger

genomes

Genomic deletions vary in size and are often slightly deleterious

Scaling of genomes and subgenomes

Genome size (Megabases)

Su

bge

nom

e si

ze (

Meg

abas

es)

Slightly deleterious amino acid substitutions accumulate in Buchnera

Correlation of drift and genome size/gene density

Shotgun sequencing of microbial genomes

Whole-genome phylogenies of prokaryotes

Evolving sequencing technologies

● Sanger Sequencing– Long (~1000 bp) reads– BUT difficult to scale up– Requires large amounts of DNA template

● ‘Next-generation’ sequencing– Shorter reads (30 – 500 bp)– Single molecule sequencing

Sequencing-by-synthesis: 454

Margulies et al. 2005 Nature

Human microbiome

Costello et al. Science (2009) 326: 1694 - 1697

Human microbiome diversity

Costello et al. Science (2009) 326: 1694 - 1697

Taxonomic diversity in the deep sea

Microbial diversity in the deep sea