International Journal of Genomics / 2020 / Article / Tab 3

Research Article

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Table 3

List of intraspecific variations of plant chloroplast genomes.

FamilySpeciesTotal length (bp)# of SNPs# of INDELsComparison samplesRef.

MarchantiaceaeMarchantia polymorpha120,288~120,30440Samples isolated in KoreaKitashirakawa-2 (Japan)[71]
00Takaragaike-1 (Japan)Kitashirakawa-2 (Japan)
69660MG762001 (Poland)Kitashirakawa-2 (Japan)
SelaginellaceaeSelaginella tamariscina126,368~126,7001,2131,641Sample isolate in KoreaSample isolate in China[74]
Selaginella uncinate144,161~144,710525602Sample isolate in JapanSample isolate in China
MagnoliaceaeMagnolia kobus159,411~159,4435050Sample isolate in Korea (Jeju Island)Sample isolate in Korea (Jeju Island)In prep.
Liriodendron tulifipera159,886120Sample isolate in KoreaSample isolate in China[52]
NymphaeaceaeNymphaea alba159,25~159,930116Sample imported in KoreaSample isolated in Germany[16]
SchisandraceaeIllicium anisatum142,723~142,74721114Sample isolated in KoreaSample isolated in USA[102]
RubiaceaeCoffea arabica155,186~155,27722Cold hardness coffee tree (CH3) planted in Jeju IslandNC_008535[62]
02Coffee tree showing high productivity (HP1) in Jeju IslandNC_008535[61]
084Coffee tree imported to Korea from Indonesia in near to 30 years ago (IN1)NC_008535[50]
38NC_008535Coffea arabica “Typica”[59]
03KY085909
04MK342634, CH3 isolate
04HP1 isolate
090IN1 isolate
36NC_008535Coffea arabica “Typica Bluemoutain”[60]
01KY085909
06MK342634, CH3 isolate
06HP1 isolate
088IN1 isolate
02Coffea arabica “Typica”
00CH1 isolateCH2 isolate[63]
TheaceaeCamellia japonica156,606~157,047252Sample isolated in Soyeonpyeong-do, Incheon, KoreaWimi-ri in Jeju, Korea[72]
78643Sample isolated in Soyeonpyeong-do, Incheon, KoreaSample isolated in China
11Sample isolated in Seogwang-ri, Jeju, KoreaSample isolated in Soyeonpyeong-do, Incheon, Korea[105]
CaryophyllaceaePseudostellaria longipedicellata149,66800Sample isolate in Mt. Taebak, KoreaSample isolate in Mt. Taebak, KoreaUnpub.
Pseudostellaria palibiniana149,639~149,66884125Sample isolated in Mt. Taebaek, KoreaSample isolated in Mt. Gwangdeok, Korea[25]
SalicaceaeSalix koriyanagi155,54800Male sample in Seoul, KoreaFemale sample in Seoul, Korea[67]
RosaceaeAgrimonia pilosa155,125258542Samples isolated in KoreaSamples isolated in China[110]
Duchesnea indica156,05045273Samples isolated in KoreaSamples isolated in China[19]
Duchesnea chrysantha156,29~156,3874858Sample isolated in KoreaSample isolated in Japan[21]
Pyrus ussuriensis159,986~160,157121781Sample isolated in Bonghwa-gun, KoreaSample isolated in Mt. Hambeak, Korea[68]
FagaceaeFagus multinervis158,34922Sample isolated in Ulleungdo Island, KoreaSample isolated in Ulleungdo Island, Korea[111]
OrobanchaceaeRehmannia glutinosa153,622~153,68014787Sample isolated in KoreaSample isolated in China[73]
CucurbitaceaeCucumis melo155,815~156,01720Cultivar TopmarkCultivar DHL92[76]
10Cultivar MR-1Cultivar DHL92
20Cultivar M4-Cultivar DHL92
10Cultivar M4Cultivar DHL92
550Cultivar M1-1Cultivar DHL92
560Cultivar M1-3Cultivar DHL92
600Cultivar M1-7Cultivar DHL92
AmaranthaceaeChenopodium quinoa6928Cultivar 0654 (Peru)Cultivar PI 614886 (Chile)[70]
3323Cultivar Cherry Vanilla (Oregon, USA)Cultivar PI 614886 (Chile)
1637Cultivar Chucapaca (Bolivia)Cultivar PI 614886 (Chile)
3623Cultivar CICA-17 (Peru)Cultivar PI 614886 (Chile)
00Cultivar G-205-95DK (Denmark)Cultivar PI 614886 (Chile)
00Cultivar Ku-2 (Chile)Cultivar PI 614886 (Chile)
3624Cultivar Kurmi (Bolivia)Cultivar PI 614886 (Chile)
3523Cultivar Ollague (Chile)Cultivar PI 614886 (Chile)
2513Cultivar Pasankalla (Peru)Cultivar PI 614886 (Chile)
1736Cultivar PI 634921 (Chile)Cultivar PI 614886 (Chile)
3724Cultivar Real (Bolivia)Cultivar PI 614886 (Chile)
30Cultivar Regalona (Chile)Cultivar PI 614886 (Chile)
3323Cultivar Salcedo INIA (Peru)Cultivar PI 614886 (Chile)
Dysphania pumilio151,960~151,962252Sample isolated in Anyang, KoreaSample isolated in Gangseo-gu, Seoul, Korea[28]
Suaeda japonica152,10933Sample isolated in Ganghwa, KoreaSample isolated in Julpo, Korea[112]
EucommiaceaeEucommia ulmoides163,341~163,5867580Sample isolated in ChinaSample isolated in China[75]
DioscoreaceaeDioscorea polystachya153,243~153,292990FLW genotypeBJXS genotype[77]
980TSW genotypeBJXS genotype
1100YTW genotypeBJXS genotype
990XSW genotypeBJXS genotype
1060NJW genotypeBJXS genotype
990MHW genotypeBJXS genotype
AsteraceaeArtemisia fukudo151,011~151,021711Sample isolated in Aphaedo, KoreaSample isolated in Jeungdo, Korea[113]
OleaceaeAbeliophyllum distichum155,982~156,0199356Sample isolated in Jincheon-gun, KoreaCultivar “Okhwang 1-ho”[90]
911Cultivar “Okhwang 1-ho”Cultivar candidate “Dae Ryun”[91]
10263Sample isolated in Jincheon-gun, KoreaCultivar candidate “Dae Ryun”
911Cultivar candidate “Dae Ryun”Cultivar candidate “Sang Jae”[92]
9356Sample isolated in Jincheon-gun, KoreaCultivar candidate “Sang Jae”
10MF407183Cultivar candidate “Sang Jae”
OrchidaceaeGoodyera schlechtendaliana153,661~154,438200511Sample isolated in Korea (MK144665)Sample isolated in Korea with different morphology (MK134679)[53]
2821,060Sample isolated in Korea (MK144665)Sample isolated in China (AB893949)
8271,794Sample isolated in Korea (MK144665)Sample isolated in China (NC_029364)
7001,066Sample isolated in Korea (MK144665)Sample isolated in China (LC085346)
163651Sample isolated in Korea with different morphology (MK134679)Sample isolated in China (AB893949)
7401,470Sample isolated in Korea with different morphology (MK134679)Sample isolated in China (NC_029364)
5971,065Sample isolated in Korea with different morphology (MK134679)Sample isolated in China (LC085346)
8442,045Sample isolated in China (AB893949)Sample isolated in China (NC_029364)
445414Sample isolated in China (AB893949)Sample isolated in China (LC085346)
7002,133Sample isolated in China (LC085346)Sample isolated in China (LC085346)
Gastrodia elata35,066~35,304457670Sample isolated in Korea (MN296709)Sample isolated in China[56]
493650Sample isolated in Korea (MN296709)Sample isolated in China[57]
324630Sample isolated in Korea (MN026874)Sample isolated in Korea (MN296709)
AdoxaceaeViburnum erosum158,587~158,6241649Sample isolated in KoreaSample isolated in Korea (MN218778)[64]
RanunculaceaeAconitum coreanum157,024~157,040517Sample isolated in KoreaSample isolated in Korea (NC_031421)[89]
2362Sample isolated in KoreaSample isolated in Korea (KU318669)
StaphyleaceaeEuscaphis japonica160,467~160,606424809Sample isolated in KoreaSample isolated in China(Oh et al., under review)
ThymelaeaceaeDaphne genkwa132,741~132,86969650Sample isolated in KoreaSample isolated in China(Oh et al., under review)

indicates that the numbers of SNPs and INDELs were inferred only from LSC, SSC, and IRb regions because one of chloroplast genomes used for comparison is partial genome.

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