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Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Methods to Compare Microbial Genomes
20 Methods to Compare Microbial Genomes
Dave UsseryBiological Sequence AnalysisDTU course # 2780327 April, 2007
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
rRNA tree
Comparative Microbial Genomics groupC
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ter fo
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eq
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ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
2. Number genes [coding density]
3. AT content
6. Repeats
4. Oligomer skews
5. Chromosome alignment
8. tRNAs and codon usage
9. Bias in codon usage
10. Amino acid usage
1. Length
7. Periodicity
Gen
om
eG
en
om
eC
od
ing
Cod
ing
20 Methods to Compare Bacterial Genomes
Comparative Microbial Genomics groupC
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ter fo
r Bio
log
ical S
eq
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ce A
naly
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e T
ech
nica
l Un
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of D
en
mark D
TU
14. Proteome comparisons
13. Blast atlases
12. Annotation quality
15. 2-D correlation of properties
16. Sigma Factors
17. Two-component systems
18. Transcription Factors
19. Membrane Proteins
20. Secreted Proteins
11. Promoters
Comparative Microbial Genomics groupC
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ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Binnewies et al., Functional and Integrative Genomics, 6:165-185 (July 2006).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
What have we learned from 300 sequenced bacterial genomes?
1. Genetic diversity is greater than we thought.
4. Generally G’s are biased towards the leading strand, but the strand bias of A’s is tax-specific.
2. Very large genomes tend to be GC-rich, whilst small genomes tend to be AT-rich.
3. There are patterns, both locally and globally of AT-richness in bacterial chromosomes.
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
1. Length
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Friis, Jensen, and Ussery
Comparative Microbial Genomics groupC
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ter fo
r Bio
log
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eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Bioinformatics, 20:3682-3686, (2004).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Microbiology, 150:749-752, (2004).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Microbiology, 150:749-752, (2004).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
tRNAs and codon usage
Microbiology, 150:1603-1605,
(2004).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Clavibacter michiganensis27% A+T content
Nitrococcus oceani50% A+T content
Wigglesworthia glossinidia78% A+T content
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
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e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Soil Bacteria
Gram +Mollicutes Enterics
Comparative Microbial Genomics groupC
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ter fo
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log
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eq
uen
ce A
naly
sis Th
e T
ech
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l Un
iversity
of D
en
mark D
TU
amino acid usage
Microbiology, 150:1603-1605,
(2004).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Bioinformatics, 20:3682-3686, (2004).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Peder Worning and Lars Juhl Jensen et al., Environmental Microbiology, 8:353-361 (Feb. 2006)
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Peder Worning and Lars Juhl Jensen et al., Environmental Microbiology, 8:353-361 (Feb. 2006)
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
P1
P2
P3
P4
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
16. Sigma Factors
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Vibrios
Gamma-Proteobacteria
Alpha, Beta, Delta, Epsilon-Proteobacteria
Firmicutes
Chlamydia
Spirochaetes
Actinobacteria
Bacteriodes
σ54
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
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ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
# ECF Sigma Factors in 250 Bacterial Genomes
Microbiology, 151:3147-3151, (2005).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
20. Secreted proteins
Vibrio
Microbiology, 151:1013-1017,
(2005).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Binnewies et al., Functional and Integrative Genomics, 6:165-185 (July 2006).
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
Comparative Microbial Genomics groupC
en
ter fo
r Bio
log
ical S
eq
uen
ce A
naly
sis Th
e T
ech
nica
l Un
iversity
of D
en
mark D
TU
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