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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.