Skip to main content

Table 1 Distribution of the protein-coding genes of host-dependent and free-living bacteria in COG functional categories

From: Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

COG functional categories

Code

OI (n = 40)

FHA (n = 85)

HD (n = 125)

FL (n = 192)

HD vs. FL

(a) Gene count Mean +/- s.d.

     

p-value*

   Chromatine structure and dynamics

B

0.28 ± 0.45

0.44 ± 1.07

0.38 ± 0.92

1.16 ± 1.28

0.4982

   Replication, recombination and repair

L

56.78 ± 26.49

161.58 ± 171.99

128.04 ± 150.56

141.23 ± 55.84

0.3035

   Transcription

K

23.70 ± 10.23

105.65 ± 74.89

79.42 ± 72.84

163.82 ± 99.52

0.0000

   RNA processing and modification

A

0.70 ± 1.26

1.20 ± 2.09

1.04 ± 1.87

1.11 ± 1.87

0.9290

   Translation, ribosomal structure and biogenesis

J

116.68 ± 13.97

143.42 ± 25.75

134.86 ± 25.83

157.62 ± 19.27

0.0000

   Posttranslational modification, protein turnover, chaperones

O

39.08 ± 10.84

74.60 ± 41.27

63.23 ± 38.31

94.13 ± 39.75

0.0000

   Intracellular trafficking, secretion, and vesicular transport

U

29.68 ± 10.05

59.62 ± 44.82

50.04 ± 39.86

63.77 ± 44.54

0.0002

   Signal transduction mechanisms

T

10.48 ± 8.45

56.65 ± 41.04

41.87 ± 40.39

103.67 ± 67.24

0.0001

   Cell cycle control, cell division, chromosome partitioning

D

11.20 ± 5.52

21.96 ± 9.96

18.52 ± 10.11

25.72 ± 7.73

0.0000

   Defense mechanisms

V

2.60 ± 4.32

20.56 ± 13.81

14.82 ± 14.35

29.46 ± 14.94

0.0000

   Cell wall/membrane/envelope biogenesis

M

39.10 ± 22.84

110.27 ± 65.03

87.50 ± 64.34

130.06 ± 59.91

0.0000

   Cell motility

N

8.23 ± 10.53

44.73 ± 44.12

33.05 ± 40.57

53.24 ± 51.60

0.0172

   Cytoskeleton

Z

0.08 ± 0.47

0.28 ± 1.09

0.22 ± 0.94

0.24 ± 0.78

0.8927

   Nucleotide transport and metabolism

F

26.70 ± 10.47

54.55 ± 19.22

45.64 ± 21.33

69.52 ± 15.52

0.0000

   Amino acid transport and metabolism

E

39.65 ± 20.39

152.06 ± 108.15

116.09 ± 104.05

213.71 ± 106.02

0.0000

   Carbohydrate transport and metabolism

G

24.05 ± 10.89

112.52 ± 86.46

84.21 ± 82.57

132.33 ± 70.07

0.0000

   Lipid transport and metabolism

I

26.15 ± 11.18

58.54 ± 45.94

48.18 ± 41.22

81.96 ± 54.49

0.0000

   Coenzyme transport and metabolism

H

40.25 ± 17.78

82.91 ± 47.76

69.26 ± 45.21

109.84 ± 39.55

0.0000

   Inorganic ion transport and metabolism

P

22.48 ± 7.80

89.40 ± 61.77

67.98 ± 59.89

127.67 ± 60.67

0.0000

   Secondary metabolites biosynthesis, transport and catabolism

Q

6.18 ± 6.09

32.34 ± 40.30

23.97 ± 35.52

50.04 ± 44.50

0.0000

   Energy production and conversion

C

48.63 ± 16.77

111.98 ± 75.61

91.70 ± 69.58

148.99 ± 82.31

0.0000

   General function prediction only

R

53.58 ± 27.82

187.75 ± 106.15

144.82 ± 108.75

265.65 ± 119.15

0.0000

   Function unknown

S

43.23 ± 27.19

184.84 ± 124.19

139.52 ± 122.80

262.59 ± 118.90

0.0000

Total

 

669.43

1867.85

1484.35

2427.53

 

(b) Percent of genes in the different functional categories (%)

Information storage and processing (B+L+K+A+J)

 

29.60

22.07

23.16

19.15

 

Cellular processes and signalling (O+U+T+D+V+M+N+Z)

 

20.98

20.81

20.83

20.61

 

Metabolism (F+E+G+I+H+P+Q+C)

 

34.97

37.17

36.85

38.48

 

Poorly characterized (R+S)

 

14.46

19.95

19.16

21.76

 
  1. OI corresponds to obligate intracellular, FHA corresponds to facultative host-associated, HD corresponds to all host-dependent, FL corresponds to free-living bacteria.
  2. *p-values < 0.05 are shown in bold to indicate significant differences between HD and FL bacteria (paired Student's t-test and Wilcoxon signed rank test)