Prokaryotic vs. eukaryotic genomes

Rocha, E Ann. Rev. Genet. 42: Genome organization in bacteria

Published by AAAS P. Glaser et al., Science 294, (2001) Comparison of two Listeria genomes Food-borne pathogen Meningitis

Phe 12s rRNA Val 16s rRNA Leu Ile Gln Met Trp Ala Asn Cys Tyr COI Ser Asp COII Lys ATP8 ATP6 COIII Gly NADH3 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 evolution Vibrio 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, 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) Subgenome size (Megabases)

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 Nature

Human microbiome Costello et al. Science (2009) 326:

Human microbiome diversity Costello et al. Science (2009) 326:

Taxonomic diversity in the deep sea

Microbial diversity in the deep sea