1. Prokaryotic vs. eukaryotic genomes

2. Rocha, E. 2008. Ann. Rev. Genet. 42: 211-233. Genome organization in bacteria

3. Published by AAAS P. Glaser et al., Science 294, 849-852 (2001) Comparison of two Listeria genomes Food-borne pathogen Meningitis

4. 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

5. The Rickettsia genome - ancestor of mitochondrial DNA

6. Plasmids and microbial evolution Vibrio cholerae genome

7. 19.10 Phylogenetic evidence for lateral gene transfer from Archaea to Entamoeba histolytica

8. Genomic turnover and HGT in the  -Proteobacteria

9. Gene expansion in microbes over time

10. Genome stasis in Buchnera

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

12. 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

13. Genomic deletions vary in size and are often slightly deleterious

14. Scaling of genomes and subgenomes Genome size (Megabases) Subgenome size (Megabases)

15. Slightly deleterious amino acid substitutions accumulate in Buchnera

16. Correlation of drift and genome size/gene density

17. Shotgun sequencing of microbial genomes

18. Whole-genome phylogenies of prokaryotes

19. 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

20. Sequencing-by-synthesis: 454 Margulies et al. 2005 Nature

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

22. Human microbiome diversity Costello et al. Science (2009) 326: 1694 - 1697

23. Taxonomic diversity in the deep sea

24. Microbial diversity in the deep sea