Summary of the variations identified in the ginseng plastomes.
| Variation type | Plastome type | 1-1 | 1-2 | 1-3 | 1-4 | 1-5 | 2 | 3-1 | 3-2 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Region | Positionz) | VariationNo.u) | 21Acc.t) | YSS | JF2 | HY1 | JYH | SH | R2 | 3Acc.s) | 3Acc.r) | JF3 | KF1 | 2Acc.q) | M1 | 3Acc.p) | 3Acc.o) | |||
| SNP | LSC | 7,159v) | S1 | G | G | G | G | G | T | G | G | G | G | G | G | G | G | G | ||
| 21,344y),v) | S2 | C | C | C | C | C | C | T | T | C | C | C | C | C | C | C | ||||
| 22,287x),v) | S3 | G | G | G | G | G | G | G | G | T | G | G | G | G | G | G | ||||
| 23,946w),v) | S4 | A | A | A | A | A | A | A | A | A | C | A | A | A | A | A | ||||
| 40,011y),w),v) | S5 | C | C | C | C | C | C | C | C | C | C | T | C | C | C | C | ||||
| 44,895w),v) | S6 | G | G | G | G | G | G | G | G | G | G | G | T | G | G | G | ||||
| IR | 90,858/151,519y),w),v) | S7 | A | A | A | A | A | A | A | A | A | A | A | A | G | A | A | |||
| SSC | 115,466 | S8 | G | G | G | G | G | T | G | G | G | G | G | G | G | G | G | |||
| 117,376x),v) | S9 | A | A | A | A | A | A | A | G | A | A | A | A | A | A | A | ||||
| 118,525y),w),v) | S10 | T | T | T | T | T | T | T | T | T | T | T | T | T | A | T | ||||
| 127,069x),v) | S11 | A | A | A | A | A | A | A | A | A | A | A | A | A | A | T | ||||
| InDel | LSC | 5,473 | ID1 | (C)8 | (C)9 | (C)8 | (C)8 | (C)8 | (C)8 | (C)9 | (C)9 | (C)8 | (C)8 | (C)8 | (C)9 | (C)8 | (C)8 | (C)8 | ||
| 7,189 | ID2 | 13×1 | 13×1 | 13×1 | 13×1 | 13×1 | 13×2 | 13×1 | 13×1 | 13×1 | 13×1 | 13×1 | 13×1 | 13×1 | 13×1 | 13×1 | ||||
| 32,850 | ID3 | 59×1 | 59×1 | 59×1 | 59×1 | 59×1 | 59×2 | 59×1 | 59×1 | 59×1 | 59×1 | 59×1 | 59×1 | 59×1 | 59×1 | 59×1 | ||||
| 38,191w) | ID4 | (C)10 | (C)10 | (C)9 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | (C)10 | ||||
| IR | 105,431/136,936 | ID5 | (G)11 | (G)11 | (G)11 | (G)10 | (G)11 | (G)10 | (G)11 | (G)11 | (G)11 | (G)11 | (G)11 | (G)11 | (G)11 | (G)11 | (G)11 | |||
| 111,304/130,897 | ID6 | 57×4 | 57×4 | 57×4 | 57×4 | 57×3 | 57×4 | 57×4 | 57×4 | 57×3 | 57×4 | 57×4 | 57×4 | 57×4 | 57×4 | 57×3 | ||||
| SSC | 115,833 | ID7 | 7×2 | 7×2 | 7×2 | 7×2 | 7×2 | 7×2 | 7×2 | 7×2 | 7×3 | 7×2 | 7×2 | 7×2 | 7×2 | 7×2 | 7×2 | |||
The nucleotides in gray boxes indicate variations. Each germplasm is represented by the abbreviation defined in
z)Variation positions are based on the plastome sequence of
y)Non-synonymous SNP.
x)Synonymous SNP.
w)Newly identified variation.
v)SNP position developed as KASP marker.
u)Variation number shown in Fig. 1.
t)ChS2, CF1, CF2, CF3, CF5, DMY, EMY, G8, G13, G17, GLS, GO, JK, JF1, JF4, JF5, R1, SP, SU, SW, and YP.
s)CS, GP, and G2.
r)CP, KF2, and KF3.
q)G15 and KF4.
p)CF4, DJ, and G16.
o)HS, JL, and KF5.
Acc.: Accessions, CDS: Coding sequence, IR: Inverted repeat, KASP: Kompetitive allele-specific PCR, LSC: Large single copy, SSC: Small single copy.
