Table 4.
Sequence polymorphism at 47 sites of nine chloroplast genome regions polymorphic among 60 accessions of melon
| Speciesa | Cluster No.b | No. of accessions | Sequence length (bp)c | Cmcp1 | Cmcp2 | Cmcp3 | Cmcp5 | ccSSR7 | Cmcp15 | PS-ID | Cmcp6 | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| SNP1 | SNP2 | SNP3 | SNP4 | SNP5 | SNP6 | SNP7 | SNP8 | SNP9 | SNP10 | SNP11 | SNP12 | SNP13 | SNP14 | SNP15 | SNP16 | SNP17 | SNP18 | SNP19 | SNP20 | SNP21 | SNP22 | SNP23 | SNP24 | |||||
| C. melo | I | a-1 | 10 | 5457 | C | C | G | C | T | C | C | G | C | T | G | T | T | G | T | A | A | A | A | C | C | C | A | G |
| C. melo | I | a-2 | 1 | 5457 | C | C | G | C | T | C | C | G | C | T | G | T | T | G | T | A | A | A | A | C | C | C | A | G |
| C. melo | I | a-3 | 5 | 5456 | C | C | G | C | T | C | C | G | C | T | G | T | T | G | T | A | A | A | A | C | C | C | A | G |
| C. melo | I | b-1 | 11 | 5479 | C | A | G | C | T | C | C | A | A | T | A | T | T | G | T | A | A | T | G | C | C | C | A | G |
| C. melo | I | b-2 | 12 | 5478 | C | A | G | C | T | C | C | A | A | T | A | T | T | G | T | A | A | T | G | C | C | C | A | G |
| C. melo | I | b-3 | 3 | 5474 | C | A | G | C | T | C | C | A | A | T | A | T | T | G | T | A | A | T | G | C | C | C | A | G |
| C. melo | I | c-1 | 1 | 5433 | T | C | C | A | G | A | C | G | C | C | G | A | C | T | T | C | C | T | G | A | C | C | A | G |
| C. melo | I | c-2 | 1 | 5472 | T | C | C | C | G | A | A | G | C | C | G | A | C | T | T | C | C | T | G | A | C | C | A | G |
| C. melo | I | c-3 | 4 | 5471 | T | C | C | C | G | A | A | G | C | C | G | A | C | T | T | C | C | T | G | A | C | C | A | A |
| C. melo | I | c-4 | 1 | 5472 | T | C | C | C | G | A | A | G | C | C | G | A | C | T | T | C | C | T | G | A | A | C | A | A |
| C. melo | I | c-5 | 5 | 5448 | C | C | C | C | G | A | C | G | C | C | G | A | C | T | C | C | C | T | G | A | C | G | G | G |
| C. melo | I | c-6 | 6 | 5455 | C | C | C | C | G | A | C | G | C | C | G | A | C | T | C | C | C | T | G | A | C | G | G | G |
| C. hystrix | II | 2 | 5468 | C | C | G | A | G | A | A | T | C | T | G | C | C | G | T | A | C | T | G | C | A | C | A | G | |
| C. hystrix | II | 1 | 5468 | C | C | G | A | G | A | A | T | C | T | G | C | A | G | T | A | C | T | G | C | A | C | A | G | |
| C. sativus | II | 1 | 5460 | C | C | G | – | G | A | C | T | C | T | G | C | C | G | T | A | C | T | G | C | A | C | A | G | |
| C. metuliferus | III | 1 | 5460 | C | C | G | C | G | A | A | G | C | T | G | C | C | G | T | A | C | T | G | C | A | C | A | A | |
| C. sagittatus | III | 1 | 5239 | C | C | G | C | G | A | C | G | C | T | G | C | C | G | G | A | C | T | – | – | A | C | A | G | |
| C. anguria | III | 1 | 5436 | C | C | G | – | G | A | C | G | C | T | G | C | C | G | G | A | A | T | G | C | A | – | A | G | |
| Speciesa | Cluster No.b | No. of ac cessions | Sequence length (bp)c | Cmcp11d | ccSSR7 | Cmcp15 | Cmcp11 | Cmcp2 | Cmcp3 | Cmcp15 | PS-ID | Cmcp6 | Cmcp11 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| SNP25 | SNP26 | SNP27 | SNP28 | SNP29 | SNP30 | InDel1 | InDel2 | InDel3 | InDel4 | InDel5 | SSR1 | SSR2 | SSR3 | SSR4 | SSR5 | SSR6 | SSR7 | SSR8 | SSR9 | SSR10 | SSR11 | SSR12 | |||||
| C. melo | I | a-1 | 10 | 5457 | G | T | G | T | G | T | 0 | 0 | +18 | +4 | −5 | (A)5 | (T)7 | (A)10 | (A)17 | (T)11 | (T)11 | (T)13 | (A)2 | (T)2 | (A)9 | (T)8 | (T)8 |
| C. melo | I | a-2 | 1 | 5457 | C | T | G | T | T | T | 0 | 0 | +18 | +4 | −5 | (A)5 | (T)7 | (A)10 | (A)17 | (T)11 | (T)11 | (T)13 | (A)2 | (T)2 | (A)9 | (T)8 | (T)8 |
| C. melo | I | a-3 | 5 | 5456 | C | T | G | T | T | T | 0 | 0 | +18 | +4 | −5 | (A)5 | (T)7 | (A)10 | (A)16 | (T)11 | (T)11 | (T)13 | (A)2 | (T)2 | (A)9 | (T)8 | (T)8 |
| C. melo | I | b-1 | 11 | 5479 | C | T | G | T | T | T | 0 | +23 | +18 | +4 | −5 | (A)5 | (T)7 | (A)10 | (A)15 | (T)11 | (T)11 | (T)14 | (A)2 | (T)2 | (A)9 | (T)8 | (T)8 |
| C. melo | I | b-2 | 12 | 5478 | C | T | G | T | T | T | 0 | +23 | +18 | +4 | −5 | (A)5 | (T)7 | (A)10 | (A)15 | (T)11 | (T)10 | (T)14 | (A)2 | (T)2 | (A)9 | (T)8 | (T)8 |
| C. melo | I | b-3 | 3 | 5474 | C | T | G | T | T | T | −5 | +23 | +18 | +4 | −5 | (A)5 | (T)7 | (A)10 | (A)15 | (T)11 | (T)11 | (T)14 | (A)2 | (T)2 | (A)9 | (T)8 | (T)8 |
| C. melo | I | c-1 | 1 | 5433 | – | C | A | G | T | C | 0 | 0 | 0 | +4 | −6 | (A)4 | (T)8 | (A)13 | (A)13 | (T)9 | (T)11 | (T)13 | (A)3 | (T)3 | (A)10 | (T)2 | (T)9 |
| C. melo | I | c-2 | 1 | 5472 | C | C | A | G | T | C | 0 | +23 | +18 | +4 | −6 | (A)4 | (T)7 | (A)12 | (A)15 | (T)9 | (T)11 | (T)13 | (A)2 | (T)2 | (A)10 | (T)2 | (T)9 |
| C. melo | I | c-3 | 4 | 5471 | C | C | A | G | T | C | 0 | +23 | +18 | +4 | −6 | (A)4 | (T)7 | (A)12 | (A)14 | (T)9 | (T)11 | (T)13 | (A)1 | (T)3 | (A)10 | (T)2 | (T)9 |
| C. melo | I | c-4 | 1 | 5472 | C | C | A | G | T | C | 0 | +23 | +18 | +4 | −6 | (A)4 | (T)7 | (A)12 | (A)14 | (T)9 | (T)11 | (T)13 | (A)1 | (T)4 | (A)10 | (T)2 | (T)9 |
| C. melo | I | c-5 | 5 | 5448 | C | C | A | G | T | C | 0 | 0 | +18 | −1 | −6 | (A)4 | (T)8 | (A)13 | (A)12 | (T)9 | (T)12 | (T)15 | (A)2 | (T)2 | (A)10 | (T)3 | (T)10 |
| C. melo | I | c-6 | 6 | 5455 | C | C | A | G | T | C | 0 | +7 | +18 | −1 | −6 | (A)4 | (T)8 | (A)13 | (A)12 | (T)9 | (T)12 | (T)15 | (A)2 | (T)2 | (A)10 | (T)3 | (T)10 |
| C. hystrix | II | 2 | 5468 | – | C | G | T | T | C | 0 | 0 | 0 | 0 | −5 | (A)3 | (T)5 | (A)9 | (A)13 | (T)9 | (T)11 | (T)12 | (A)2 | (T)5 | (A)13 | (T)2 | (T)9 | |
| C. hystrix | II | 1 | 5468 | – | C | G | T | T | C | 0 | 0 | 0 | 0 | −5 | (A)3 | (T)5 | (A)9 | (A)13 | (T)9 | (T)11 | (T)12 | (A)2 | (T)5 | (A)13 | (T)2 | (T)9 | |
| C. sativus | II | 1 | 5460 | – | C | G | T | T | C | 0 | 0 | 0 | 0 | −5 | (A)3 | (T)6 | (A)9 | (A)14 | (T)9 | (T)11 | (T)11 | (A)2 | (T)5 | (A)15 | (T)2 | (T)8 | |
| C. metuliferus | III | 1 | 5460 | – | C | G | T | T | C | 0 | 0 | 0 | −1 | 0 | (A)3 | (T)6 | (A)18 | (A)14 | (T)12 | (T)5 | (T)9 | (A)2 | (T)4 | (A)11 | (T)2 | (T)10 | |
| C. sagittatus | III | 1 | 5239 | – | C | G | T | T | C | 0 | 0 | 0 | 0 | 0 | (A)3 | (T)6 | (A)17 | (A)11 | (T)15 | (T)8 | (T)9 | – | – | (A)12 | (T)2 | (T)12 | |
| C. anguria | III | 1 | 5436 | – | C | G | T | T | C | 0 | −7 | 0 | 0 | 0 | (A)3 | (T)6 | (A)14 | (A)14 | (T)13 | (T)11 | (T)8 | (A)2 | (T)4 | (A)10 | (T)2 | (T)11 | |
a
Single nucleotide polymorphism, insertion or deletion and simple sequence repeat are represented by “SNP”, “In/Del” and “SSR”, respectively. SNPs data of wild species was also indicated. Absence of sequence at SNP and SSR sites was indicated by “−”.
b
Cluster number refers to Fig. 1.
c
Sequence length indicating total number of nucleotides of nine chloroplast genome regions.
d
SNP25 was located in the motif sequence of In/Del3.