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Table 4 Presence of variable length symbiosis-related genes in each phenotype cluster of S. meliloti and S. medicae

From: Comparative genomics of the core and accessory genomes of 48 Sinorhizobiumstrains comprising five genospecies

 

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)

   noeJ 1 K 1

5 (1)

0

0

0

   noeJ 2 K 2

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

    

   exoF 2

26 (5)

14 (2)

  

   exoI

95 (18)

100 (14)

0

0

   exoI 2

32 (6)

36 (5)

0

0

   exoP 2

26 (5)

14 (2)

0

0

   exoW

100 (19)

93 (13)

100 (11)

100 (2)

Galactoglucan (EPS II) biosynthesis

    

   expD 2

95 (18)

86 (12)

100 (11)

100 (2)

   expE 8

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

   rkpRSTZ 1

100 (19)

93 (13)

100 (11)

100 (2)

   rkpT 2

84 (16)

86 (12)

100 (11)

100 (2)

   rkpZ 2

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, virD 2 , 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

    

   hemA 2

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

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

ISSN: 1474-760X

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