Plant Breeding and Biotechnology

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Table. 1.

Table. 1.

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 rps16trnQ-UUG 7,159v) S1 G G G G G T G G G G G G G G G
rpoC2 CDS 21,344y),v) S2 C C C C C C T T C C C C C C C
rpoC1 CDS 22,287x),v) S3 G G G G G G G G T G G G G G G
rpoC1 intron 23,946w),v) S4 A A A A A A A A A C A A A A A
psaB CDS 40,011y),w),v) S5 C C C C C C C C C C T C C C C
ycf3 intron 44,895w),v) S6 G G G G G G G G G G G T G G G
IR ycf2 CDS 90,858/151,519y),w),v) S7 A A A A A A A A A A A A G A A
SSC ndhFrpl32 115,466 S8 G G G G G T G G G G G G G G G
ccsA CDS 117,376x),v) S9 A A A A A A A G A A A A A A A
ndhD CDS 118,525y),w),v) S10 T T T T T T T T T T T T T A T
ycf1 CDS 127,069x),v) S11 A A A A A A A A A A A A A A T
InDel LSC rps16 intron 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
rps16trnQ-UUG 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
trnE-UUCtrnT- GGU 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
psbZtrnG-UCC 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 trnA-UGC intron 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
ycf1 CDS 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 rpl32trnL-UAG 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 Supplementary Table 2.

z)Variation positions are based on the plastome sequence of P. ginseng cv. ‘Chunpoong’ (KM088019).

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.

Plant Breed. Biotech. 2022;10:174-85 https://doi.org/10.9787/PBB.2022.10.3.174
© 2022 Plant Breed. Biotech.