Table 4.
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.