Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome...
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Transcript of Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome...
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Prokaryotic vs. eukaryotic genomes
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Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233.
Genome organization in bacteria
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Published by AAAS
P. Glaser et al., Science 294, 849-852 (2001)
Comparison of two Listeria genomes
• Food-borne pathogen• Meningitis
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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
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The Rickettsia genome - ancestor of mitochondrial DNA
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Plasmids and microbial evolutionVibrio cholerae genome
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19.10 Phylogenetic evidence for lateral gene transfer from Archaea to Entamoeba histolytica
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Genomic turnover and HGT in the -Proteobacteria
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Gene expansion in microbes over time
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Genome stasis in Buchnera
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Buchnera and ancestral enteric bacteria (E. coli)Gray areas area ancestral genomic components lost
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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
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Genomic deletions vary in size and are often slightly deleterious
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Scaling of genomes and subgenomes
Genome size (Megabases)
Su
bge
nom
e si
ze (
Meg
abas
es)
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Slightly deleterious amino acid substitutions accumulate in Buchnera
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Correlation of drift and genome size/gene density
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Shotgun sequencing of microbial genomes
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Whole-genome phylogenies of prokaryotes
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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
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Sequencing-by-synthesis: 454
Margulies et al. 2005 Nature
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Human microbiome
Costello et al. Science (2009) 326: 1694 - 1697
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Human microbiome diversity
Costello et al. Science (2009) 326: 1694 - 1697
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Taxonomic diversity in the deep sea
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Microbial diversity in the deep sea