1. MICROBIOLOGIA GENERALE Prokaryotic genomes

2. The Escherichia coli nucleoid

3. The chromosome of Escherichia coli

5. Autoradiograph of intact replicating chromosome of Escherichia coli

6. The prokaryotic genome Prokaryotes sometimes possess smaller extrachromosomal pieces of DNA called plasmids.The total DNA content of a prokaryote is referred to as the cell genome

7. The prokaryotic genome

8. Core genome versus Pan genome

9. Essential and non-essential genes in the prokaryotic genome

13. Supercoiled DNA

15. Prokaryotic genomes: Sequencing, sizes, ORF contents and gene distributions

16. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Fleischmann et al. Science 269, 469-512, 1995 An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism. H. influenzae DNA was sonicated and fragments with sizes between 1.6 and 2.0 kb purified from an agarose gel and ligated into a plasmid vector to produce a clone library. End sequences were obtained from clones taken from this library, and a computer used to identify overlaps between sequences. This resulted in 140 sequence contigs, which were assembled into the complete genome sequence,

17. The steps in a whole-genome shotgun sequencing project

20. How does the computer find an ORF?

21. Locating possible functional open reading frames (ORFs)

22. Escherichia coli genomes: core genome and pathogenic islands Green: genes common to all strains Red: genes present in the pathogenic strains only Blue: genes found only in uropathogen strain 536

24. How Many Genomes Have Been Sequenced? March 10, 2015 (NCBI) Archaea: 469 Bacteria: 31731 Protists: 266 Animals: 557 Plants: 218

27. MicroorganismSize (bp)ORFs Mycoplasma genitalium 580 070470 Borrelia burgdorferi 910 725853 Treponema pallidum1 138 0061041 Helicobacter pylori1 667 8671590 Staphylococcus aureus2 814 8162593 Bacillus subtilis4 214 8104100 Mycobacterium tuberculosis4 411 5293924 Escherichia coli4 639 2214288 Pseudomonas aeruginosa6 264 4035570 Streptomyces coelicolor8 667 5077846 Prokaryotic genomes

28. Genome size (megabases) Total ORFs in genome Correlation between genome size and ORF content in prokaryotes Each megabase of prokaryotic DNA encodes about 1000 ORFs

29. Gene function in bacteria genomes

30. Functional category of genes as a relative percent of the genome versus total ORFs in the genome

31. Variations in gene category in Bacteria and Archea

32. OrganismSize (Mbp)ORFs Saccharomyces cerevisiae 13 (16 chr)5570 Plasmodium falciparum 27 (14 chr)- Encephalitozoon cuniculi2.9 (11 chr)1997 Caenorhabditis elegans97 (6 chr)19099 Arabidopsis thaliana125 (5 chr)25498 Mus musculus2500 (23 chr)30000 Homo sapiens3000 (23 chr)30000? Eukaryotic genomes

35. Bacterial metagenomics

36. How complete microbial genome sequence data can speed vaccine development