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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