Genomic Data (Accession)  

Cornejo, O.E., Muh-Ching Yee, Victor Dominguez, Mary Andrews, Alexandra Sockell, Erika Strandberg, Donald Livingstone III, Conrad Stack, Alberto Romero, Pathmanathan Umaharan, Stefan Royaert, Nilesh R. Tawari, Pauline Ng, Osman Gutierrez, Wilbert Phillips, Keithanne Mockaitis, Carlos D. Bustamante & Juan C. Motamayor (2018) Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process. Commun Biol 1, 167

SampleNameClone nameRunExperimentBioSampleSampleSourceTree ID
AGU_3339_12AGU 3339 /12 [CHA]SRR7774183SRX4629641SAMN09934393Trinidad18276
AM_1_54AM 1 /54 [POU]SRR7774305SRX4629519SAMN09934400Costa Rica-
AM_2_18AM 2 /18 [POU]SRR7774304SRX4629520SAMN09934401Costa Rica-
AMAZ_12AMAZ 12SRR7774307SRX4629517SAMN09934398Trinidad17443
AMAZ_15_15AMAZ 15 /15SRR7774306SRX4629518SAMN09934399Trinidad17421
AMAZ-11_G18_A1AMAZ 11SRR7774243SRX4629581SAMN09934394Ecuador-
AMAZ-11_G21_A10AMAZ 11SRR7774242SRX4629582SAMN09934395Ecuador-
AMAZ-14_G23_A1AMAZ 14SRR7774309SRX4629515SAMN09934396Ecuador-
AMAZ-14_G24_A5AMAZ 14SRR7774308SRX4629516SAMN09934397Ecuador-
BE_10BE 10SRR7774303SRX4629521SAMN09934402Costa Rica17422
BR25BR 25SRR7774302SRX4629522SAMN09934403Indonesia (gDNA USDA)-
Brisas-1BRISAS 1SRR7774178SRX4629646SAMN09934406(Ecuador) gDNA USDATc02491
CAB_71_PL3CAB 71SRR7774179SRX4629645SAMN09934407gDNA MiamiTc02565
CAB_76_PL3CAB 76SRR7774176SRX4629648SAMN09934408gDNA MiamiTc02567
CAB_77_PL5CAB 77SRR7774177SRX4629647SAMN09934409gDNA MiamiTc02568
CATIE_1000CATIE 1000SRR7800376SRX4629650SAMN09934410Costa Rica17423
CatongoCATONGOSRR7774215SRX4629609SAMN09934430Costa Rica17445
CC_71CC 71SRR7774352SRX4629472SAMN09934418Costa Rica-
CCAT1119_EET544_A1EET 544 [ECU]SRR7774175SRX4629649SAMN09934411Ecuador-
CCAT1858_EET547EET 547 [ECU]SRR7774172SRX4629652SAMN09934412Ecuador-
CCAT4675_EET575EET 575 [ECU]SRR7774173SRX4629651SAMN09934413Ecuador-
CCAT4688_EET576_A1EET 576 [ECU]SRR7774181SRX4629643SAMN09934414Ecuador-
CCAT4998_EET577EET 577 [ECU]SRR7774182SRX4629642SAMN09934415Ecuador-
CCN10CCN 10SRR7774350SRX4629474SAMN09934416Costa Rica17446
CCN51CCN 51SRR7774349SRX4629475SAMN09934417Brazil, MARS-
CL_27_50CL 27 /50SRR7774351SRX4629473SAMN09934419TrinidadTc17482
COCA_3370_5COCA 3370 /5 [CHA]SRR7774346SRX4629478SAMN09934420Costa RicaTc04611
criolloCRIOLLO [CRI]SRR7774278SRX4629546SAMN09934580Costa Rica-
CRU_101CRU 101SRR7774348SRX4629476SAMN09934422TrinidadTc17492
CRU_59CRU 59SRR7774347SRX4629477SAMN09934423Trinidad-
CRU_89CRU 89SRR7774355SRX4629469SAMN09934424TrinidadTc17488
CRUZ_7_14CRUZ 7 /14SRR7774345SRX4629479SAMN09934421Costa Rica-
CUR3_G35_A1CUR 3 [CHA]SRR7774159SRX4629665SAMN09934426Ecuador-
CUR3_G37_A6CUR 3 [CHA]SRR7774157SRX4629667SAMN09934427Ecuador-
CUR3_G38_A8CUR 3 [CHA]SRR7774170SRX4629654SAMN09934428Ecuador-
CUR3_G39_A10CUR 3 [CHA]SRR7774226SRX4629598SAMN09934429Ecuador-
EB2237_A1EB 2237SRR7774156SRX4629668SAMN09934432Ecuador-
EET_103EET 103 [ECU]SRR7774210SRX4629614SAMN09934441Ecuador17424
EET_395SILECIA 8 [ECU]SRR7774209SRX4629615SAMN09934442Trinidad18186
EET_400EET 400 [ECU]SRR7774208SRX4629616SAMN09934443Costa RicaTc17439
EET_58EET 58 [ECU]SRR7774213SRX4629611SAMN09934444TrinidadTc17727
EET_59EET 59 [ECU]SRR7774212SRX4629612SAMN09934445Trinidad18302
EET103_BordeEET 103 [ECU]SRR7774158SRX4629666SAMN09934433Ecuador17424
EET397EET 397 [ECU]SRR7774241SRX4629583SAMN09934434Costa Rica17447
EET400_Arbol-122EET 400 [ECU]SRR7774342SRX4629482SAMN09934435EcuadorTc21291
EET446_A1EET 446 [ECU]SRR7774207SRX4629617SAMN09934436Ecuador-
EET451_A1EET 451 [ECU]SRR7774206SRX4629618SAMN09934437Ecuador-
EET462_A1EET 462 [ECU]SRR7774205SRX4629619SAMN09934438Ecuador-
EET58_A1EET 58 [ECU]SRR7774204SRX4629620SAMN09934439Ecuador-
EET95_A2EET 95 [ECU]SRR7774211SRX4629613SAMN09934440Ecuador-
ELP_20_AELP 20 ASRR7774268SRX4629556SAMN09934446Costa RicaTc02198
FSC_13FSC 13SRR7774269SRX4629555SAMN09934447Costa Rica18315
GU_114_PGU 114 /PSRR7774267SRX4629557SAMN09934449TrinidadTc17459
GU_175_PGU 175 /PSRR7774254SRX4629570SAMN09934450TrinidadTc17460
GU_222GU 222SRR7774270SRX4629554SAMN09934452Trinidad-
GU_300_PGU 300 /PSRR7774271SRX4629553SAMN09934453TrinidadTc17463
GU_307GU 307SRR7774227SRX4629597SAMN09934454Costa Rica17426
GU_308AGU 308 /ASRR7774228SRX4629596SAMN09934455Costa RicaTc02175
GU255_VGU 255 /VSRR7774266SRX4629558SAMN09934448Costa Rica17425
ICA_70ICA 70 [COL]SRR7774255SRX4629569SAMN09934456Trinidad18321
ICS_1ICS 1SRR7774310SRX4629514SAMN09934459leaf from Miami-
ICS_43ICS 43SRR7774313SRX4629511SAMN09934460Trinidad18331
ICS_6ICS 6SRR7774312SRX4629512SAMN09934461TrinidadTc00551
ICS_60ICS 60SRR7774315SRX4629509SAMN09934462TrinidadTc18242
ICS_61ICS 61SRR7774314SRX4629510SAMN09934463Trinidad-
ICS_95ICS 95SRR7774230SRX4629594SAMN09934464gDNA MiamiTc16546
ICS39ICS 39SRR7774299SRX4629525SAMN09934457Costa Rica17448
ICS40ICS 40SRR7774311SRX4629513SAMN09934458Costa Rica17449
IMC_12IMC 12SRR7774328SRX4629496SAMN09934466Trinidad18339
IMC_14IMC 14SRR7774329SRX4629495SAMN09934467Trinidad17733
IMC_20IMC 20SRR7774330SRX4629494SAMN09934468TrinidadTc00707
IMC_36IMC 36SRR7774257SRX4629567SAMN09934469TrinidadTc00709
IMC_47IMC 47SRR7774274SRX4629550SAMN09934470Costa RicaTc16547
IMC_50IMC 50SRR7774285SRX4629539SAMN09934471TrinidadTc00560
IMC_51IMC 51SRR7774343SRX4629481SAMN09934472TrinidadTc00753
IMC67IMC 67SRR7774229SRX4629595SAMN09934465TrinidadTc17736
JA_5_35JA 5 /35 [POU]SRR7774344SRX4629480SAMN09934473Trinidad-
JA_5_36JA 5 /36 [POU]SRR7774327SRX4629497SAMN09934474Trinidad-
JA_5_5JA 5 /5 [POU]SRR7774331SRX4629493SAMN09934475Trinidad-
KA2KA 2SRR7774202SRX4629622SAMN09934477Papua New Guinea-
LCT_EEN_46LCT EEN 46SRR7774192SRX4629632SAMN09934480TrinidadTc01431
LCT_EEN_83_S-8LCT EEN 83 /S-8SRR7774297SRX4629527SAMN09934481Trinidad-
LCT46_A1LCT EEN 46SRR7774201SRX4629623SAMN09934478Ecuador-
LCTEEN_141LCT EEN 141SRR7774326SRX4629498SAMN09934479gDNA MiamiTc01453
LP_3_40LP 3 /40 [POU]SRR7774187SRX4629637SAMN09934482Trinidad18348
LP_4_48LP 4 /48 [POU]SRR7774185SRX4629639SAMN09934483Trinidad-
LX_32LX 32SRR7774214SRX4629610SAMN09934484Costa Rica-
LX_43LX 43SRR7774296SRX4629528SAMN09934485Costa Rica-
M_8M 8 [SUR]SRR7774292SRX4629532SAMN09934499Trinidad-
MAN_15_2MAN 15 /2 [BRA]SRR7774258SRX4629566SAMN09934492Costa Rica17428
MatinaMATINASRR7774287SRX4629537SAMN09934500Costa Rica-
MO_109MO 109SRR7774272SRX4629552SAMN09934494TrinidadTc18213
MO_4MO 4SRR7774273SRX4629551SAMN09934495Trinidad18362
MO_9MO 9SRR7774291SRX4629533SAMN09934496Trinidad18370
MO_99MO 99SRR7774290SRX4629534SAMN09934497TrinidadTc17508
MocorongoMOCORONGOSRR7774286SRX4629538SAMN09934501Costa Rica17429
mvP30P 30 [POS]SRR7774277SRX4629547SAMN09934581--
mvT85T 85 [POS]SRR7774280SRX4629544SAMN09934582Indonesia-
MXC_67MXC 67SRR7774293SRX4629531SAMN09934498Trinidad18391
NA_286NA 286SRR7774295SRX4629529SAMN09934504Trinidad18395
NA_33_T2NA 33SRR7774222SRX4629602SAMN09934506TrinidadTc00797
NA_331NA 331SRR7774294SRX4629530SAMN09934505TrinidadTc00923
NA_712NA 712SRR7774223SRX4629601SAMN09934507TrinidadTc0629
NA_92NA 92SRR7774224SRX4629600SAMN09934508TrinidadTc00657
NA45NA 45SRR7774289SRX4629535SAMN09934502Costa RicaTc00602
NA702NA 702SRR7774288SRX4629536SAMN09934503TrinidadTC0930
OC_61OC 61 [VEN]SRR7774219SRX4629605SAMN09934511TrinidadTc17475
PA_107PA 107 [PER]SRR7774216SRX4629608SAMN09934514Trinidad18407
PA_120PA 120 [PER]SRR7774217SRX4629607SAMN09934515TrinidadTc18221
PA_121PA 121 [PER]SRR7774236SRX4629588SAMN09934516Costa Rica, gDNA from MiamiTc00955
PA_13PA 13 [PER]SRR7774235SRX4629589SAMN09934517gDNA MiamiTc18218
PA_137PA 137 [PER]SRR7774234SRX4629590SAMN09934518TrinidadTc15958
PA_150PA 150 [PER]SRR7774233SRX4629591SAMN09934519TrinidadTC00501
PA_169PA 169 [PER]SRR7774240SRX4629584SAMN09934520TrinidadTc15974
PA_218PA 218 [PER]SRR7774239SRX4629585SAMN09934521Trinidad18192
PA_51PA 51 [PER]SRR7774238SRX4629586SAMN09934522MiamiTc00686
PA_56PA 56 [PER]SRR7774237SRX4629587SAMN09934523Trinidad18396
PA_70PA 70 [PER]SRR7774232SRX4629592SAMN09934524gDNA MiamiTc15954
PA_88PA 88 [PER]SRR7774231SRX4629593SAMN09934525gDNA MiamiTC00983
PA107_A1PA 107 [PER]SRR7774220SRX4629604SAMN09934512Trinidad-
PA289PA 289 [PER]SRR7774221SRX4629603SAMN09934513TrinidadTc00511
PBC123PBC 123SRR7774164SRX4629660SAMN09934526Indonesia (gDNA USDA)-
PlayaAlta1PLAYA ALTA 1 [VEN]SRR7774169SRX4629655SAMN09934531TrinidadTc16545
POUND_10_BPOUND 10 /BSRR7774163SRX4629661SAMN09934529TrinidadTc00858
Pound_7POUND 7SRR7774166SRX4629658SAMN09934532Costa Rica-
POUND_7_BPOUND 7 /BSRR7774168SRX4629656SAMN09934530Trinidad18419
RB_40RB 40 [BRA]SRR7774160SRX4629664SAMN09934534Costa RicaTc00449
RB_47_PL3RB 47 [BRA]SRR7774161SRX4629663SAMN09934535Costa RicaTc02518
RB39PL1RB 39 [BRA]SRR7774167SRX4629657SAMN09934533Costa RicaTc02522
REDAMEL_1_27REDAMEL 1 /27SRR7774194SRX4629630SAMN09934536Trinidad18180
REDAMEL_1_31REDAMEL 1 /31SRR7774193SRX4629631SAMN09934537Trinidad-
SC_1SC 1 [COL]SRR7774190SRX4629634SAMN09934544Costa Rica-
SCA_10SCA 10SRR7774195SRX4629629SAMN09934539TrinidadTc00984
SCA_11SCA 11SRR7774198SRX4629626SAMN09934540TrinidadTc00882
SCA_19SCA 19SRR7774197SRX4629627SAMN09934541Costa RicaTc00522
SCA_24.2SCA 24SRR7774200SRX4629624SAMN09934542Costa RicaTc00523
SCA_5SCA 5SRR7774199SRX4629625SAMN09934543gDNA MiamiTc00884
SCA6**SCA 6SRR7774196SRX4629628SAMN09934538gDNA MiamiTc16548
SIAL169SIAL 169SRR7774189SRX4629635SAMN09934545Costa RicaTc00179
SIAL70SIAL 70SRR7774316SRX4629508SAMN09934546Costa RicaTc00185
SIAL84SIAL 84SRR7774317SRX4629507SAMN09934547Costa RicaTc00186
SIC806SIC 806SRR7774318SRX4629506SAMN09934548Costa RicaTc00200
SIL-1_G56_A6SIL 1SRR7774319SRX4629505SAMN09934549Costa Rica-
SJ_2_22SJ 2 /22 [POU]SRR7774320SRX4629504SAMN09934550Trinidad18442
SLC_4SLC 4SRR7774321SRX4629503SAMN09934551TrinidadTc17513
SNA0707SNA 707SRR7774322SRX4629502SAMN09934552Costa Rica-
sp1SP 1 [VEN]SRR7774279SRX4629545SAMN09934583Venezuela (gDNA USDA)-
SPA_7SPA 7 [COL]SRR7774323SRX4629501SAMN09934553Costa Rica-
SPEC_194_75SPEC 194 /75SRR7774324SRX4629500SAMN09934554TrinidadTc18235
SPEC_54_1SPEC 54 /1SRR7774325SRX4629499SAMN09934555Costa RicaTc05194
T675_A645_A1A 645 [ECU]SRR7774341SRX4629483SAMN09934556Ecuador-
T678_B60_A1B 60 [ECU]SRR7774340SRX4629484SAMN09934557Ecuador-
T684_EET233_A1EET 233 [ECU]SRR7774337SRX4629487SAMN09934560Ecuador-
T685_EET387_A1EET 387 [ECU]SRR7774336SRX4629488SAMN09934561Ecuador-
T686_LCT-368_A1LCT EEN 368SRR7774335SRX4629489SAMN09934562Ecuador-
T695_SCA-6_A1SCA 6SRR7774334SRX4629490SAMN09934563Ecuador-
TAP10_G12_A1TAP 10 [CHA]SRR7774333SRX4629491SAMN09934564Ecuador-
TAP3_G70_A2TAP 3 [CHA]SRR7774332SRX4629492SAMN09934565Ecuador-
TAP6_G12_A1TAP 6 [CHA]SRR7774252SRX4629572SAMN09934566Ecuador-
TIP-1_G41_A1TIPUTINI 1 [CHA]SRR7774253SRX4629571SAMN09934567Ecuador-
TRD_45TRD 45SRR7774191SRX4629633SAMN09934569Trinidad18443
TRD86TRD 86SRR7774188SRX4629636SAMN09934568Trinidad-
TSA654ZymoTSA 654SRR7774248SRX4629576SAMN09934570Costa Rica17457
TSH1188TSH 1188SRR7774249SRX4629575SAMN09934571Brazil, MARS-
TSH516TSH 516SRR7774246SRX4629578SAMN09934572Costa Rica17455
UF_11UF 11SRR7774282SRX4629542SAMN09934576Costa Rica18446
UF_668UF 668SRR7774281SRX4629543SAMN09934577Costa Rica17456
UF_676UF 676SRR7774284SRX4629540SAMN09934578Costa RicaTc13037
UF12UF 12SRR7774247SRX4629577SAMN09934573Costa Rica17434
UF273_T1UF 273SRR7774244SRX4629580SAMN09934574Costa Rica-
UF273_T2UF 273SRR7774245SRX4629579SAMN09934575Costa Rica-
UNAP2_G78_A2UNAP 2 [CHA]SRR7774283SRX4629541SAMN09934579Ecuador-