Table 3.
Comparisons of mutation changes, number of synonymous (S) and nonsynonymous (N) substitutions per gene of protein-coding genes among four Alpinia chloroplast genomes.
| Genes | A. katsumadai |
A. oxyphylla Guangdong |
A. zerumbet |
A. oxyphylla Hainan |
Location | ||||
|---|---|---|---|---|---|---|---|---|---|
| S | N | S | N | S | N | S | N | ||
| psbA | 3 | 0 | 3 | 0 | 3 | 0 | 3 | 0 | LSC |
| matK | 2 | 1 | 3 | 3 | 2 | 2 | 3 | 3 | LSC |
| atpA | 1 | 1 | 2 | 1 | 1 | 1 | 2 | 1 | LSC |
| atpF | - | - | - | - | 2 | 0 | - | - | LSC |
| atpH | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | LSC |
| atpI | 1 | 1 | - | - | 2 | 1 | - | - | LSC |
| rps2 | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | LSC |
| rpoC2 | 5 | 7 | 8 | 8 | 6 | 7 | 8 | 8 | LSC |
| rpoC1 | 0 | 2 | 6 | 3 | 0 | 2 | 6 | 3 | LSC |
| rpoB | 7 | 2 | 7 | 3 | 6 | 3 | 7 | 3 | LSC |
| petN | - | - | - | - | 1 | 0 | - | - | LSC |
| psbD | - | - | - | - | 1 | 2 | - | - | LSC |
| psbC | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | LSC |
| psbZ | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | LSC |
| rps14 | - | - | 0 | 1 | 1 | 0 | 0 | 1 | LSC |
| psaB | 2 | 0 | 2 | 1 | 1 | 0 | 2 | 1 | LSC |
| psaA | 6 | 1 | 4 | 1 | 5 | 1 | 4 | 1 | LSC |
| ycf3 | - | - | 1 | 0 | - | - | 1 | 0 | LSC |
| rps4 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | LSC |
| ndhK | 0 | 2 | 1 | 1 | 1 | 3 | 1 | 1 | LSC |
| ndhC | 1 | 1 | 0 | 2 | 0 | 1 | 0 | 2 | LSC |
| atpB | - | - | 2 | 2 | 1 | 1 | 3 | 2 | LSC |
| rbcL | 3 | 4 | 5 | 1 | 3 | 3 | 5 | 1 | LSC |
| accD | 2 | 1 | 3 | 2 | 2 | 1 | 3 | 2 | LSC |
| ycf4 | - | - | 1 | 0 | - | - | 1 | 0 | LSC |
| cemA | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | LSC |
| petA | 0 | 2 | 1 | 2 | 0 | 2 | 1 | 2 | LSC |
| rpl33 | - | - | 0 | 1 | - | - | 0 | 1 | LSC |
| rps18 | - | - | 1 | 0 | - | - | 1 | 0 | LSC |
| rpl20 | - | - | 2 | 0 | 1 | 0 | 2 | 0 | LSC |
| clpP | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | LSC |
| psbB | 1 | 0 | - | - | 3 | 0 | - | - | LSC |
| psbH | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | LSC |
| petB | 1 | 0 | - | - | 1 | 0 | - | - | LSC |
| petD | - | - | 0 | 1 | - | - | 0 | 1 | LSC |
| rpoA | 1 | 0 | 0 | 1 | - | - | 0 | 1 | LSC |
| rps11 | - | - | 0 | 1 | - | - | 0 | 1 | LSC |
| rpl36 | 1 | 0 | 2 | 0 | 1 | 0 | 2 | 0 | LSC |
| infA | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | LSC |
| rps8 | 2 | 0 | 2 | 0 | 2 | 0 | 2 | 0 | LSC |
| rpl14 | 1 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | LSC |
| rpl16 | - | - | - | - | 0 | 1 | - | - | LSC |
| rps3 | 3 | 2 | 2 | 3 | 2 | 3 | 2 | 3 | LSC |
| rpl22 | 0 | 3 | 0 | 1 | 0 | 3 | 0 | 1 | LSC |
| ndhF | 5 | 7 | 8 | 5 | 6 | 6 | 8 | 5 | SSC |
| ccsA | 0 | 3 | 0 | 2 | 1 | 2 | 0 | 2 | SSC |
| ndhD | - | - | 3 | 0 | - | - | 3 | 0 | SSC |
| ndhE | - | - | 1 | 0 | - | - | 1 | 0 | SSC |
| ndhG | 2 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | SSC |
| ndhI | - | - | 1 | 0 | - | - | 1 | 0 | SSC |
| ndhA | 2 | 2 | 2 | 1 | 2 | 2 | 2 | 1 | SSC |
| ndhH | 2 | 2 | 1 | 0 | 2 | 2 | 1 | 0 | SSC |
| rps15 | 1 | 1 | 0 | 3 | 0 | 1 | 0 | 3 | SSC |
| ycf1 | 2 | 15 | 6 | 19 | 3 | 18 | 6 | 19 | IRa/b |
| Total | 67 | 61 | 90 | 72 | 73 | 69 | 91 | 72 | - |