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.