1. Nothing in (computational) biology makes
Comparative genomics and the new perspective on genome evolution
Nothing in (computational) biology makes
sense except in the light of evolution
after Theodosius Dobzhansky (1970)

3. Conservation of gene order in bacterial species of the same genus1
101
201
301
401
501
601
M. genitalium vs
M. pneumoniae

4. Conservation of gene order in closely related bacterial genera1
101
201
301
401
501
601
701
801
901
1001
C. trachomatis vs
C. pneumoniae

5. Lack of gene order conservation - even in “closely related” bacteria of the same Proteobacterial subdivision
P. aeruginosa vs
E. coli

6. Genome Alignments - Method
Protein sets from completely genomes
BLAST cross-comparison
Table of Hits
Pairwise Genome Alignment
Local alignment algorithm
Lamarck (gap opening penalty,
gap extension penalty); statistics
with Monte Carlo simulations
Template-Anchored Genome Alignment

8. Genome Alignments - Statistics
0.0
0.1
0.2
0.3
0.4
0.5 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
>20
cpneu-ctra
mjan-mthe
bsub-ecoli
drad-aero
Distribution of conserved gene string lengths

9. Genome Alignments - Statistics
Pairwise No. No. % in % in
alignments: strings genes Gen1 Gen2
all homologs
ecoli-hinf % 33%
ecoli-bsub % 8%
ecoli-mjan % 2%
probable orthologs
ecoli-hinf % 28%
ecoli-bsub % 4%
ecoli-mjan % 2%

10. Genome Alignments - Statistics
500
1000
1500
2000
2500
3000
3500
4000
4500
5000
aero
aful
mjan
mthe
pyro
aquae
bbur
bsub
cac
cjej
cpneu
ctra
drad
ecoli
hinf
hpyl
mgen
mpneu
mtub
nmen
rpxx
synecho
tmar
tpal
uure
Not in gene strings
In non-conserved gene strings (directons)
In conserved gene strings
Breakdown of genes
in the genome

11. Genome Alignments - Statistics
Fraction of the genome in conserved gene strings - from
template-anchored alignments
Minimum Synechocystis sp. 5%
Aquifex aeolicus 10%
Archaeoglobus fulgidus 13%
Escherichia coli 14%
Treponema pallidum 17%
Maximum Thermotoga maritima 23%
Mycoplasma genitalium 24%

12. The three domains of life: the Tree
-proteobacteria
-proteobacteria
-proteobacteria
spirochetes
Bacteria
chlamydias
Bacillus/Clostridium group
mycoplasmas
actinobacteria
Dra
cyanobacteria
Aae
Tma
Mth
Mja
Pxx
Archaea
Txx
Afu
crenarchaea
Hbs
eukaryota

19. The three domains of life: relationships within clusters of orthologs
(COGs)
Eukaryotes A
245
496
Bacteria
A+B
1882
729
111
A+B+E
1087
Archaea
A+E
315
Pan-archaeal COGs
All COGs

20. Protein functions in the archaeo-eukaryotic and
archaeo-bacterial subsets of the conserved archaeal core
(310 COGs total)

21. Phylogenetic trees of aminoacyl-tRNA synthetases:
HGT comes out loud and clear
Eco E
Sce E cyt
Ath E cyt
Hsa Q
Sce Q
Eco Q
Hin Q
Mth E
Mja E
Pho E
Afu E
Sso E
Hpy E /1/
Hpy E /2/
Hin E
Tpa E
Bbu E
Cel E mit
Sce E mit
Ctr E
Mtu E
Ssp E
Mpn E
Mge E
Bsu E
Aae E
Mge W
Mpn W
Sce W mit
Cel W mit
Ssp W
Hpy W
Bsu W
Mtu W
Hin W
Eco W
Aae W
Ctr W
Tpa W
Bbu W
Afu W
Mth W
Mja W
Pho W
Sce W cyt
Hsa W cyt

22. Eukaryotic programmed cell death - the bacterial contribution
PC_Hsa
Csp1_Hsa
Mlr1804_Mlo
PC_Cel
Csp2_Hsa
CED3_Cel
Mlr3463_Mlo
Mll5190_Mlo
Csp10_Hsa
Mll2372_Mlo
Mlr2366_Mlo
Csp3_Hsa
Mlr3303_Mlo
Csp9_Hsa
CASP-like_Deha
Gingipain R_Pgin
PC_Ddis
ActD_Mxan
XF2779_Xfa
Gingipain K_Pgin
Mlr3300_Mlo
YOR197w_Sce
PK3_Scoe
MC1_At
MC_Spo
MC_Geos
MC3_At
MC5_At
MC_Rsph
MC_Hbr
MC4_At
MC2_At
Phylogenetic tree of the caspase-like protease superfamily

24. Inconsistency Quotient
IQ = minimal number of events (Loss, Emergence, or HGT)
required to reconcile a COG’s phyletic pattern with
the topology of the species tree
A B C D
A B C D
A B C D
IQ=1
IQ=1
IQ=2
IQ=2
A B C D
2 parsimonious
scenarios
Loss
HGT

25. Number of gene loss and HGT events in most parsimonious
evolutionary scenarios for COGs (I values).

26. Conclusion
Comparative genomics shows that genome evolution
is a highly dynamic process dominated by gene shuffling,
lineage-specific gene loss and horizontal gene transfer