Supporting Information
Appendix S1: More information on the robust regression method used in this
study
Figure S1: SIGI-HMM predictions in 54 Escherichia coli strains
The left panel shows SIGI-HMM predictions (cyan regions) from the genomes of 54 E.
coli strains, colored blue according to genomic %AT from light blue (most AT rich) to
dark blue (most GC rich). The horizontal axis designates the chromosomal position in
base pairs (bp), while the vertical axis to the right indicates total size of predicted GIs
(bp). The right panel shows more detailed annotations of E. coli O26:H11 strain 11368,
the E. coli with the largest genome, and E. coli K-12 substrain MG1655, a non-pathogenic
model organism with one of the smallest E. coli genomes. Genes ending with an
underscore indicate multiple variants of the gene. ECO26_P_ designates multiple
variants of E. coli O26:H11 prophages. More details regarding these annotations can be
found in tables S5 and S6 for E. coli K-12 and E. coli O26:H11, respectively. Graphical
representation dissimilarities of HT regions between the genomes in the left and right
panels are due to scale differences.
Table S1: Results from phylum level genome size versus AT content robust
regression analysis
The table includes regression estimates (column 2) for the bacteria in each phylogenetic
group and Proteobacteria subphyla (column 1) as well as standard error (column 3), tstatistic (column 4), p values (column 5) and number n of strains included in the
analysis (column 6).
Group/subphyla
Actinobacteria
Estimate Std. Error
-17,54
1,24
Firmicutes
-0,75
Tenericutes
0,25
Bacteroides-Chlorobi
T
p
n
-14,2
0,0001
214
0,75
-1
0,32
423
0,57
0,44
0,66
54
-5,55
2,16
-2,57
0,01
93
Alpha-proteobacteria
-7,86
0,39
-20,02
0,0001
215
Beta-proteobacteria
-8,26
0,76
-10,81
0,0001
120
Delta-proteobacteria
-4,36
1,69
-2,58
0,01
43
0,43
0,19
2,2
0,03
74
-10,88
0,48
-22,77
0,0001
429
Epsilon-proteobacteria
Gamma-proteobacteria
Chlamydiae-Verrucombia
5,75
0,01
673,46
0,0001
49
Cyanobacteria
-3,83
2,29
-1,67
0,1
44
Spirochaetes
-2,56
1,66
-1,54
0,15
47
Table S2: Result from species level genomic size vs AT content robust regression
analysis
The table shows the results from regression analyses between genome size and
genomic %AT in the strains of the designated species in column 1. Column 2 shows the
regression estimates, column 3 - standard error, column 4 - t statistic, column 5 - p value
and column 6 the number n of strains included in each regression model.
Species
Estimate
Std. Error
t
p
n
Chlamydia trachomatis
20,56
1,34
15,34
0,0001
21
Neisseria meningitides
17,1
5,29
3,34
0,006
14
Helicobacter pylori
11,45
3,76
3,04
0,004
38
149,64
22,21
6,74
0,0001
54
-2,7
44,59
-0,06
0,95
25
-103,5
45,82
-2,26
0,04
12
Acinetobacter baumannii
2,17
31,89
0,07
0,95
10
Francisella tularensis
2,88
0,31
9,34
0,0001
10
Buchnera aphidicola
0,02
0,01
2,23
0,05
11
Bacillus cereus
0,48
8,6
0,06
0,95
18
Escherichia coli
Salmonella enterica
Yersinia pestis
Clostridium botulinum
-28,02
8,31
-3,37
0,006
13
Listeria monocytogenes
47,27
7,56
6,25
0,0001
22
Staphylococcus aureus
-11,8
12,58
-0,94
0,35
31
33,3
12,9
2,58
0,02
19
33,16
8,66
3,83
0,002
14
10,5
12,99
0,81
0,43
16
0,6
0,52
1,16
0,27
14
-19,05
11,65
-1,64
0,13
13
Corynebacterium pseudotuberculosis
-50,1
8,79
-5,7
0,0001
15
Prochlorococcus marinus
-3,59
0,32 -11,22
0,0001
12
Streptococcus pneumoniae
Streptococcus suis
Streptococcus pyogenes
Mycobacterium tuberculosis
Corynebacterium diphtheriae
Table S3 - Robust regression analysis of relative entropy versus genomic %AT species level
The table shows the results from regression analyses between genome-based relative
entropy and genomic %AT in the strains of the designated species in column 1. Column
2 shows the regression estimates, column 3 - standard error, column 4 - t statistic,
column 5 - p value and column 6 the number n of strains included in each regression
model.
Species
Estimate
Std. Error
T
p
n
Chlamydia trachomatis
0,05
0,08
0,67
0,51
21
Neisseria meningitides
-0,5
0,06
-7,72
0,0001
14
Helicobacter pylori
-0,04
0,12
-0,34
0,74
38
Escherichia coli
-0,67
0,06
-12,17
0,0001
54
Salmonella enterica
-1,04
0,04
-23,91
0,0001
26
Yersinia pestis
-0,03
0,14
-0,22
0,83
12
0,01
0,1
0,05
0,96
10
Francisella tularensis
0,2
0,07
2,94
0,02
10
Buchnera aphidicola
0,24
1,00E-03
158,37
0,0001
11
Acinetobacter baumannii
Bacillus cereus
-0,07
0,07
-1,12
0,28
18
0,72
0,06
12,62
0,0001
13
Listeria monocytogenes
-0,55
0,04
-13,31
0,0001
22
Staphylococcus aureus
0,05
0,05
0,9
0,38
31
Streptococcus pneumoniae
-0,24
0,07
-3,19
0,005
19
Streptococcus suis
-0,12
0,09
-1,43
0,18
14
0,01
0,12
0,1
0,92
16
Mycobacterium tuberculosis
-0,06
1,60E-03
-36,58
0,0001
14
Corynebacterium diphtheriae
-0,04
0,09
-0,46
0,65
13
0,09
0,06
1,46
0,17
15
-0,03
0,01
-2,43
0,04
12
Clostridium botulinum
Streptococcus pyogenes
Corynebacterium pseudotuberculosis
Prochlorococcus marinus
Table S4 - Robust regression analysis of relative entropy versus genome size species level
The table shows the results from regression analyses between genome-based relative
entropy and genome size in the strains of the designated species in column 1. Column 2
shows the regression estimate, column 3 - standard error, column 4 - t statistic, column
5 - p value and column 6 the number n of strains included in each regression model.
Species
Estimate
Std. Error
T
p
Chlamydia trachomatis
-7,78
0,79
-9,79
Neisseria meningitidis
-32,69
8,52
Helicobacter pylori
-20,69
4,84
-280,34
n
0,0001
21
-3,84
0,002
14
-4,27
0,0001
38
21,97
-12,76
0,0001
54
26,41
23,84
1,11
0,28
26
107,03
126,28
0,85
0,42
12
-133,97
108,25
-1,24
0,25
10
Francisella tularensis
-1,63
6,43
-0,25
0,81
10
Buchnera aphidicola
0,05
3,00E-02
1,75
0,11
11
Bacillus cereus
-245,54
32,23
-7,62
0,0001
18
Clostridium botulinum
-127,68
3,45
-37,05
0,0001
13
Listeria monocytogenes
-124,06
13,44
-9,23
0,0001
22
Staphylococcus aureus
-203,96
14,61
-13,96
0,0001
31
Streptococcus pneumoniae
-133,67
22,91
-5,83
0,0001
19
-82,33
43,49
-1,89
0,08
14
-87,4
11,58
-7,55
0,0001
16
0,27
2,30E-01
1,17
0,26
14
Escherichia coli
Salmonella enterica
Yersinia pestis
Acinetobacter baumannii
Streptococcus suis
Streptococcus pyogenes
Mycobacterium tuberculosis
Corynebacterium diphtheriae
Corynebacterium pseudotuberculosis
Prochlorococcus marinus
-25,97
48,16
-0,54
0,6
13
-335,35
13,55
-24,75
0,0001
15
-25,02
5,28
-4,74
0,0008
12
Table S5 - Annotations of SIGI-HMM predicted regions in Escherichia coli K-12
substrain MG1655 in Excel format
NCBI name and chromosome position of SIGI-HMM predictions are found in the first
column, with more detailed explanation of the predicted DNA in columns 2 and 3. All
annotations are taken from the Islandviewer web-site.
Table S6 - Annotations of SIGI-HMM predicted regions in Escherichia coli O26:H11
strain 11368 in Excel format
NCBI name and chromosome position of SIGI-HMM predictions are found in the first
column, with more detailed explanation of the predicted DNA in columns 2 and 3. All
annotations are taken from the Islandviewer web-site.