Transcript Prokaryotic genomes

MICROBIOLOGIA GENERALE
Prokaryotic genomes
The Escherichia coli nucleoid
The chromosome of Escherichia coli
The chromosome of Escherichia coli
Autoradiograph of intact replicating chromosome of
Escherichia coli
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
The prokaryotic genome
Core genome versus Pan genome
Essential and non-essential genes in the prokaryotic genome
Supercoiled DNA
Prokaryotic genomes:
Sequencing, sizes, ORF
contents and gene
distributions
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,
The steps in a whole-genome shotgun sequencing project
How does the computer find an ORF?
Locating possible functional open reading frames (ORFs)
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
How Many Genomes Have Been Sequenced?
March 10, 2015 (NCBI)
Archaea: 469
Bacteria: 31731
Protists: 266
Animals: 557
Plants: 218
Prokaryotic genomes
Microorganism
Mycoplasma genitalium
Borrelia burgdorferi
Size (bp)
ORFs
580 070
910 725
470
853
Treponema pallidum
1 138 006
1041
Helicobacter pylori
Staphylococcus aureus
1 667 867
2 814 816
1590
2593
Bacillus subtilis
Mycobacterium tuberculosis
4 214 810
4 411 529
4100
3924
Escherichia coli
Pseudomonas aeruginosa
4 639 221
6 264 403
4288
5570
Streptomyces coelicolor
8 667 507
7846
Total ORFs in genome
Correlation between genome size and ORF content in prokaryotes
Genome size (megabases)
Each megabase of prokaryotic DNA encodes about 1000 ORFs
Gene function in bacteria genomes
Functional category of genes as a relative percent of the
genome versus total ORFs in the genome
Variations in gene category in Bacteria and Archea
Eukaryotic genomes
Organism
Saccharomyces cerevisiae
Plasmodium falciparum
Encephalitozoon cuniculi
Size (Mbp)
13 (16 chr)
27 (14 chr)
ORFs
5570
-
2.9 (11 chr)
1997
97 (6 chr)
19099
Arabidopsis thaliana
Mus musculus
125 (5 chr)
2500 (23 chr)
25498
30000
Homo sapiens
3000 (23 chr)
30000?
Caenorhabditis elegans
Eukaryotic genomes
Bacterial metagenomics
How complete microbial genome sequence data can speed vaccine development