Table 4

Presence of variable length symbiosis-related genes in each phenotype cluster of S. meliloti and S. medicae

Species and phenotype cluster (PC)a


S. meliloti

S. medicae



Gene or gene cluster

I (n = 19)

II (n = 14)

I (n = 11)

II (n = 2)


Nodulation

nodN

95 (18)

64 (9)

0

0

noeA

100 (19)

93 (13)

100 (11)

100 (2)

noeJ1K1

5 (1)

0

0

0

noeJ2K2

0

0

9 (1)

0

noeLnolK

5 (1)

0

0

0

Nitrogen fixation

fixQ

100 (19)

86 (12)

100 (11)

100 (2)

fixR

100 (19)

93 (13)

0

0

fixU

95 (18)

79 (11)

100 (11)

100 (2)

nifD

100 (19)

100 (14)

100 (11)

50 (1)

nifE

100 (19)

100 (14)

90 (10)

100 (2)

Succinoglycan (EPS I) biosynthesis

exoF2

26 (5)

14 (2)

exoI

95 (18)

100 (14)

0

0

exoI2

32 (6)

36 (5)

0

0

exoP2

26 (5)

14 (2)

0

0

exoW

100 (19)

93 (13)

100 (11)

100 (2)

Galactoglucan (EPS II) biosynthesis

expD2

95 (18)

86 (12)

100 (11)

100 (2)

expE8

95 (18)

100 (14)

100 (11)

100 (2)

Cyclic β-glucan biosynthesis

cgmB

0

7 (1)

0

0

Capusular polysaccharide biosynthesis

rkpLMNOPQ

16 (3)

7 (1)

0

0

rkpRSTZ1

100 (19)

93 (13)

100 (11)

100 (2)

rkpT2

84 (16)

86 (12)

100 (11)

100 (2)

rkpZ2

16 (3)

14 (2)

0

0

Type III secretion system

T3SSa: rhc, nolUV

26 (5)

29 (4)

0

0

Type IV secretion system

T4SSa: rctA, vir

100 (19)

100 (14)

0

0

T4SSb: vir

47 (9)

0

100 (11)

0

T4SSd: tra, trb

0

7 (1)

100 (11)

100 (2)

T4SSe: tra, trb, virD2, cogG

0

14 (2)

0

0

T4SSf: avh

37 (7)

71 (10)

18 (2)

0

T4SSg: tra, trb

0

7 (1)

0

0

Denitrification

napEFDABC

100 (19)

93 (13)

100 (11)

100 (2)

nirKV

84 (16)

29 (4)

82 (9)

0

norECBQD

84 (16)

29 (4)

82 (9)

0

nosRZDFYLX

89 (17)

36 (5)

0

Heme biosynthesis

hemA2

16 (3)

29 (4)

0

0

hemN

74 (14)

36 (5)

73 (8)

0

1-Aminocyclopropane-1-carboxylate deaminase

acdS (Smed_5532 ortholog)

21 (4)

0

36 (4)

100 (2)

acdS (Smed_6456 ortholog)

5 (1)

36 (5)

36 (4)

0


aThe percentage and number (in parentheses) of strains possessing a gene or gene cluster are shown for each species group and phenotype cluster.

Sugawara et al. Genome Biology 2013 14:R17   doi:10.1186/gb-2013-14-2-r17

Open Data