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Prokaryotic vs. eukaryotic genomes

Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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Page 1: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Prokaryotic vs. eukaryotic genomes

Page 2: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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

Genome organization in bacteria

Page 3: 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

Page 4: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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

Page 5: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

The Rickettsia genome - ancestor of mitochondrial DNA

Page 6: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Plasmids and microbial evolutionVibrio cholerae genome

Page 7: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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

Page 8: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Genomic turnover and HGT in the -Proteobacteria

Page 9: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Gene expansion in microbes over time

Page 10: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Genome stasis in Buchnera

Page 11: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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

Page 12: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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

Page 13: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Genomic deletions vary in size and are often slightly deleterious

Page 14: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Scaling of genomes and subgenomes

Genome size (Megabases)

Su

bge

nom

e si

ze (

Meg

abas

es)

Page 15: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Slightly deleterious amino acid substitutions accumulate in Buchnera

Page 16: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Correlation of drift and genome size/gene density

Page 17: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Shotgun sequencing of microbial genomes

Page 18: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Whole-genome phylogenies of prokaryotes

Page 19: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

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

Page 20: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Sequencing-by-synthesis: 454

Margulies et al. 2005 Nature

Page 21: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Human microbiome

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

Page 22: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Human microbiome diversity

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

Page 23: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Taxonomic diversity in the deep sea

Page 24: Prokaryotic vs. eukaryotic genomes. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

Microbial diversity in the deep sea