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
SampleName | Clone name | Run | Experiment | BioSample | SampleSource | Tree ID |
---|---|---|---|---|---|---|
AGU_3339_12 | AGU 3339 /12 [CHA] | SRR7774183 | SRX4629641 | SAMN09934393 | Trinidad | 18276 |
AM_1_54 | AM 1 /54 [POU] | SRR7774305 | SRX4629519 | SAMN09934400 | Costa Rica | - |
AM_2_18 | AM 2 /18 [POU] | SRR7774304 | SRX4629520 | SAMN09934401 | Costa Rica | - |
AMAZ_12 | AMAZ 12 | SRR7774307 | SRX4629517 | SAMN09934398 | Trinidad | 17443 |
AMAZ_15_15 | AMAZ 15 /15 | SRR7774306 | SRX4629518 | SAMN09934399 | Trinidad | 17421 |
AMAZ-11_G18_A1 | AMAZ 11 | SRR7774243 | SRX4629581 | SAMN09934394 | Ecuador | - |
AMAZ-11_G21_A10 | AMAZ 11 | SRR7774242 | SRX4629582 | SAMN09934395 | Ecuador | - |
AMAZ-14_G23_A1 | AMAZ 14 | SRR7774309 | SRX4629515 | SAMN09934396 | Ecuador | - |
AMAZ-14_G24_A5 | AMAZ 14 | SRR7774308 | SRX4629516 | SAMN09934397 | Ecuador | - |
BE_10 | BE 10 | SRR7774303 | SRX4629521 | SAMN09934402 | Costa Rica | 17422 |
BR25 | BR 25 | SRR7774302 | SRX4629522 | SAMN09934403 | Indonesia (gDNA USDA) | - |
Brisas-1 | BRISAS 1 | SRR7774178 | SRX4629646 | SAMN09934406 | (Ecuador) gDNA USDA | Tc02491 |
CAB_71_PL3 | CAB 71 | SRR7774179 | SRX4629645 | SAMN09934407 | gDNA Miami | Tc02565 |
CAB_76_PL3 | CAB 76 | SRR7774176 | SRX4629648 | SAMN09934408 | gDNA Miami | Tc02567 |
CAB_77_PL5 | CAB 77 | SRR7774177 | SRX4629647 | SAMN09934409 | gDNA Miami | Tc02568 |
CATIE_1000 | CATIE 1000 | SRR7800376 | SRX4629650 | SAMN09934410 | Costa Rica | 17423 |
Catongo | CATONGO | SRR7774215 | SRX4629609 | SAMN09934430 | Costa Rica | 17445 |
CC_71 | CC 71 | SRR7774352 | SRX4629472 | SAMN09934418 | Costa Rica | - |
CCAT1119_EET544_A1 | L11-H19 [ECU] | SRR7774175 | SRX4629649 | SAMN09934411 | Ecuador | - |
CCAT1858_EET547 | L18-H58 [ECU] | SRR7774172 | SRX4629652 | SAMN09934412 | Ecuador | - |
CCAT4675_EET575 | L46-H75 [ECU] | SRR7774173 | SRX4629651 | SAMN09934413 | Ecuador | - |
CCAT4688_EET576_A1 | L46-H88 [ECU] | SRR7774181 | SRX4629643 | SAMN09934414 | Ecuador | - |
CCAT4998_EET577 | L49-H98 [ECU] | SRR7774182 | SRX4629642 | SAMN09934415 | Ecuador | - |
CCN10 | CCN 10 | SRR7774350 | SRX4629474 | SAMN09934416 | Costa Rica | 17446 |
CCN51 | CCN 51 | SRR7774349 | SRX4629475 | SAMN09934417 | Brazil, MARS | - |
CL_27_50 | CL 27 /50 | SRR7774351 | SRX4629473 | SAMN09934419 | Trinidad | Tc17482 |
COCA_3370_5 | COCA 3370 /5 [CHA] | SRR7774346 | SRX4629478 | SAMN09934420 | Costa Rica | Tc04611 |
criollo | CRIOLLO [CRI] | SRR7774278 | SRX4629546 | SAMN09934580 | Costa Rica | - |
CRU_101 | CRU 101 | SRR7774348 | SRX4629476 | SAMN09934422 | Trinidad | Tc17492 |
CRU_59 | CRU 59 | SRR7774347 | SRX4629477 | SAMN09934423 | Trinidad | - |
CRU_89 | CRU 89 | SRR7774355 | SRX4629469 | SAMN09934424 | Trinidad | Tc17488 |
CRUZ_7_14 | CRUZ 7 /14 | SRR7774345 | SRX4629479 | SAMN09934421 | Costa Rica | - |
CUR3_G35_A1 | CUR 3 [CHA] | SRR7774159 | SRX4629665 | SAMN09934426 | Ecuador | - |
CUR3_G37_A6 | CUR 3 [CHA] | SRR7774157 | SRX4629667 | SAMN09934427 | Ecuador | - |
CUR3_G38_A8 | CUR 3 [CHA] | SRR7774170 | SRX4629654 | SAMN09934428 | Ecuador | - |
CUR3_G39_A10 | CUR 3 [CHA] | SRR7774226 | SRX4629598 | SAMN09934429 | Ecuador | - |
EB2237_A1 | EB 2237 | SRR7774156 | SRX4629668 | SAMN09934432 | Ecuador | - |
EET_103 | EET 103 [ECU] | SRR7774210 | SRX4629614 | SAMN09934441 | Ecuador | 17424 |
EET_395 | SILECIA 8 [ECU] | SRR7774209 | SRX4629615 | SAMN09934442 | Trinidad | 18186 |
EET_400 | EET 400 [ECU] | SRR7774208 | SRX4629616 | SAMN09934443 | Costa Rica | Tc17439 |
EET_58 | EET 58 [ECU] | SRR7774213 | SRX4629611 | SAMN09934444 | Trinidad | Tc17727 |
EET_59 | EET 59 [ECU] | SRR7774212 | SRX4629612 | SAMN09934445 | Trinidad | 18302 |
EET103_Borde | EET 103 [ECU] | SRR7774158 | SRX4629666 | SAMN09934433 | Ecuador | 17424 |
EET397 | EET 397 [ECU] | SRR7774241 | SRX4629583 | SAMN09934434 | Costa Rica | 17447 |
EET400_Arbol-122 | EET 400 [ECU] | SRR7774342 | SRX4629482 | SAMN09934435 | Ecuador | Tc21291 |
EET446_A1 | EET 446 [ECU] | SRR7774207 | SRX4629617 | SAMN09934436 | Ecuador | - |
EET451_A1 | EET 451 [ECU] | SRR7774206 | SRX4629618 | SAMN09934437 | Ecuador | - |
EET462_A1 | EET 462 [ECU] | SRR7774205 | SRX4629619 | SAMN09934438 | Ecuador | - |
EET58_A1 | EET 58 [ECU] | SRR7774204 | SRX4629620 | SAMN09934439 | Ecuador | - |
EET95_A2 | EET 95 [ECU] | SRR7774211 | SRX4629613 | SAMN09934440 | Ecuador | - |
ELP_20_A | ELP 20 A | SRR7774268 | SRX4629556 | SAMN09934446 | Costa Rica | Tc02198 |
FSC_13 | FSC 13 | SRR7774269 | SRX4629555 | SAMN09934447 | Costa Rica | 18315 |
GU_114_P | GU 114 /P | SRR7774267 | SRX4629557 | SAMN09934449 | Trinidad | Tc17459 |
GU_175_P | GU 175 /P | SRR7774254 | SRX4629570 | SAMN09934450 | Trinidad | Tc17460 |
GU_222 | GU 222 | SRR7774270 | SRX4629554 | SAMN09934452 | Trinidad | - |
GU_300_P | GU 300 /P | SRR7774271 | SRX4629553 | SAMN09934453 | Trinidad | Tc17463 |
GU_307 | GU 307 | SRR7774227 | SRX4629597 | SAMN09934454 | Costa Rica | 17426 |
GU_308A | GU 308 /A | SRR7774228 | SRX4629596 | SAMN09934455 | Costa Rica | Tc02175 |
GU255_V | GU 255 /V | SRR7774266 | SRX4629558 | SAMN09934448 | Costa Rica | 17425 |
ICA_70 | ICA 70 [COL] | SRR7774255 | SRX4629569 | SAMN09934456 | Trinidad | 18321 |
ICS_1 | ICS 1 | SRR7774310 | SRX4629514 | SAMN09934459 | leaf from Miami | - |
ICS_43 | ICS 43 | SRR7774313 | SRX4629511 | SAMN09934460 | Trinidad | 18331 |
ICS_6 | ICS 6 | SRR7774312 | SRX4629512 | SAMN09934461 | Trinidad | Tc00551 |
ICS_60 | ICS 60 | SRR7774315 | SRX4629509 | SAMN09934462 | Trinidad | Tc18242 |
ICS_61 | ICS 61 | SRR7774314 | SRX4629510 | SAMN09934463 | Trinidad | - |
ICS_95 | ICS 95 | SRR7774230 | SRX4629594 | SAMN09934464 | gDNA Miami | Tc16546 |
ICS39 | ICS 39 | SRR7774299 | SRX4629525 | SAMN09934457 | Costa Rica | 17448 |
ICS40 | ICS 40 | SRR7774311 | SRX4629513 | SAMN09934458 | Costa Rica | 17449 |
IMC_12 | IMC 12 | SRR7774328 | SRX4629496 | SAMN09934466 | Trinidad | 18339 |
IMC_14 | IMC 14 | SRR7774329 | SRX4629495 | SAMN09934467 | Trinidad | 17733 |
IMC_20 | IMC 20 | SRR7774330 | SRX4629494 | SAMN09934468 | Trinidad | Tc00707 |
IMC_36 | IMC 36 | SRR7774257 | SRX4629567 | SAMN09934469 | Trinidad | Tc00709 |
IMC_47 | IMC 47 | SRR7774274 | SRX4629550 | SAMN09934470 | Costa Rica | Tc16547 |
IMC_50 | IMC 50 | SRR7774285 | SRX4629539 | SAMN09934471 | Trinidad | Tc00560 |
IMC_51 | IMC 51 | SRR7774343 | SRX4629481 | SAMN09934472 | Trinidad | Tc00753 |
IMC67 | IMC 67 | SRR7774229 | SRX4629595 | SAMN09934465 | Trinidad | Tc17736 |
JA_5_35 | JA 5 /35 [POU] | SRR7774344 | SRX4629480 | SAMN09934473 | Trinidad | - |
JA_5_36 | JA 5 /36 [POU] | SRR7774327 | SRX4629497 | SAMN09934474 | Trinidad | - |
JA_5_5 | JA 5 /5 [POU] | SRR7774331 | SRX4629493 | SAMN09934475 | Trinidad | - |
KA2 | KA 2 | SRR7774202 | SRX4629622 | SAMN09934477 | Papua New Guinea | - |
LCT_EEN_46 | LCT EEN 46 | SRR7774192 | SRX4629632 | SAMN09934480 | Trinidad | Tc01431 |
LCT_EEN_83_S-8 | LCT EEN 83 /S-8 | SRR7774297 | SRX4629527 | SAMN09934481 | Trinidad | - |
LCT46_A1 | LCT EEN 46 | SRR7774201 | SRX4629623 | SAMN09934478 | Ecuador | - |
LCTEEN_141 | LCT EEN 141 | SRR7774326 | SRX4629498 | SAMN09934479 | gDNA Miami | Tc01453 |
LP_3_40 | LP 3 /40 [POU] | SRR7774187 | SRX4629637 | SAMN09934482 | Trinidad | 18348 |
LP_4_48 | LP 4 /48 [POU] | SRR7774185 | SRX4629639 | SAMN09934483 | Trinidad | - |
LX_32 | LX 32 | SRR7774214 | SRX4629610 | SAMN09934484 | Costa Rica | - |
LX_43 | LX 43 | SRR7774296 | SRX4629528 | SAMN09934485 | Costa Rica | - |
M_8 | M 8 [SUR] | SRR7774292 | SRX4629532 | SAMN09934499 | Trinidad | - |
MAN_15_2 | MAN 15 /2 [BRA] | SRR7774258 | SRX4629566 | SAMN09934492 | Costa Rica | 17428 |
Matina | MATINA | SRR7774287 | SRX4629537 | SAMN09934500 | Costa Rica | - |
MO_109 | MO 109 | SRR7774272 | SRX4629552 | SAMN09934494 | Trinidad | Tc18213 |
MO_4 | MO 4 | SRR7774273 | SRX4629551 | SAMN09934495 | Trinidad | 18362 |
MO_9 | MO 9 | SRR7774291 | SRX4629533 | SAMN09934496 | Trinidad | 18370 |
MO_99 | MO 99 | SRR7774290 | SRX4629534 | SAMN09934497 | Trinidad | Tc17508 |
Mocorongo | MOCORONGO | SRR7774286 | SRX4629538 | SAMN09934501 | Costa Rica | 17429 |
mvP30 | P 30 [POS] | SRR7774277 | SRX4629547 | SAMN09934581 | - | - |
mvT85 | T 85 [POS] | SRR7774280 | SRX4629544 | SAMN09934582 | Indonesia | - |
MXC_67 | MXC 67 | SRR7774293 | SRX4629531 | SAMN09934498 | Trinidad | 18391 |
NA_286 | NA 286 | SRR7774295 | SRX4629529 | SAMN09934504 | Trinidad | 18395 |
NA_33_T2 | NA 33 | SRR7774222 | SRX4629602 | SAMN09934506 | Trinidad | Tc00797 |
NA_331 | NA 331 | SRR7774294 | SRX4629530 | SAMN09934505 | Trinidad | Tc00923 |
NA_712 | NA 712 | SRR7774223 | SRX4629601 | SAMN09934507 | Trinidad | Tc0629 |
NA_92 | NA 92 | SRR7774224 | SRX4629600 | SAMN09934508 | Trinidad | Tc00657 |
NA45 | NA 45 | SRR7774289 | SRX4629535 | SAMN09934502 | Costa Rica | Tc00602 |
NA702 | NA 702 | SRR7774288 | SRX4629536 | SAMN09934503 | Trinidad | TC0930 |
OC_61 | OC 61 [VEN] | SRR7774219 | SRX4629605 | SAMN09934511 | Trinidad | Tc17475 |
PA_107 | PA 107 [PER] | SRR7774216 | SRX4629608 | SAMN09934514 | Trinidad | 18407 |
PA_120 | PA 120 [PER] | SRR7774217 | SRX4629607 | SAMN09934515 | Trinidad | Tc18221 |
PA_121 | PA 121 [PER] | SRR7774236 | SRX4629588 | SAMN09934516 | Costa Rica, gDNA from Miami | Tc00955 |
PA_13 | PA 13 [PER] | SRR7774235 | SRX4629589 | SAMN09934517 | gDNA Miami | Tc18218 |
PA_137 | PA 137 [PER] | SRR7774234 | SRX4629590 | SAMN09934518 | Trinidad | Tc15958 |
PA_150 | PA 150 [PER] | SRR7774233 | SRX4629591 | SAMN09934519 | Trinidad | TC00501 |
PA_169 | PA 169 [PER] | SRR7774240 | SRX4629584 | SAMN09934520 | Trinidad | Tc15974 |
PA_218 | PA 218 [PER] | SRR7774239 | SRX4629585 | SAMN09934521 | Trinidad | 18192 |
PA_51 | PA 51 [PER] | SRR7774238 | SRX4629586 | SAMN09934522 | Miami | Tc00686 |
PA_56 | PA 56 [PER] | SRR7774237 | SRX4629587 | SAMN09934523 | Trinidad | 18396 |
PA_70 | PA 70 [PER] | SRR7774232 | SRX4629592 | SAMN09934524 | gDNA Miami | Tc15954 |
PA_88 | PA 88 [PER] | SRR7774231 | SRX4629593 | SAMN09934525 | gDNA Miami | TC00983 |
PA107_A1 | PA 107 [PER] | SRR7774220 | SRX4629604 | SAMN09934512 | Trinidad | - |
PA289 | PA 289 [PER] | SRR7774221 | SRX4629603 | SAMN09934513 | Trinidad | Tc00511 |
PBC123 | PBC 123 | SRR7774164 | SRX4629660 | SAMN09934526 | Indonesia (gDNA USDA) | - |
PlayaAlta1 | PLAYA ALTA 1 [VEN] | SRR7774169 | SRX4629655 | SAMN09934531 | Trinidad | Tc16545 |
POUND_10_B | POUND 10 /B | SRR7774163 | SRX4629661 | SAMN09934529 | Trinidad | Tc00858 |
Pound_7 | POUND 7 | SRR7774166 | SRX4629658 | SAMN09934532 | Costa Rica | - |
POUND_7_B | POUND 7 /B | SRR7774168 | SRX4629656 | SAMN09934530 | Trinidad | 18419 |
RB_40 | RB 40 [BRA] | SRR7774160 | SRX4629664 | SAMN09934534 | Costa Rica | Tc00449 |
RB_47_PL3 | RB 47 [BRA] | SRR7774161 | SRX4629663 | SAMN09934535 | Costa Rica | Tc02518 |
RB39PL1 | RB 39 [BRA] | SRR7774167 | SRX4629657 | SAMN09934533 | Costa Rica | Tc02522 |
REDAMEL_1_27 | REDAMEL 1 /27 | SRR7774194 | SRX4629630 | SAMN09934536 | Trinidad | 18180 |
REDAMEL_1_31 | REDAMEL 1 /31 | SRR7774193 | SRX4629631 | SAMN09934537 | Trinidad | - |
SC_1 | SC 1 [COL] | SRR7774190 | SRX4629634 | SAMN09934544 | Costa Rica | - |
SCA_10 | SCA 10 | SRR7774195 | SRX4629629 | SAMN09934539 | Trinidad | Tc00984 |
SCA_11 | SCA 11 | SRR7774198 | SRX4629626 | SAMN09934540 | Trinidad | Tc00882 |
SCA_19 | SCA 19 | SRR7774197 | SRX4629627 | SAMN09934541 | Costa Rica | Tc00522 |
SCA_24.2 | SCA 24 | SRR7774200 | SRX4629624 | SAMN09934542 | Costa Rica | Tc00523 |
SCA_5 | SCA 5 | SRR7774199 | SRX4629625 | SAMN09934543 | gDNA Miami | Tc00884 |
SCA6** | SCA 6 | SRR7774196 | SRX4629628 | SAMN09934538 | gDNA Miami | Tc16548 |
SIAL169 | SIAL 169 | SRR7774189 | SRX4629635 | SAMN09934545 | Costa Rica | Tc00179 |
SIAL70 | SIAL 70 | SRR7774316 | SRX4629508 | SAMN09934546 | Costa Rica | Tc00185 |
SIAL84 | SIAL 84 | SRR7774317 | SRX4629507 | SAMN09934547 | Costa Rica | Tc00186 |
SIC806 | SIC 806 | SRR7774318 | SRX4629506 | SAMN09934548 | Costa Rica | Tc00200 |
SIL-1_G56_A6 | SIL 1 | SRR7774319 | SRX4629505 | SAMN09934549 | Costa Rica | - |
SJ_2_22 | SJ 2 /22 [POU] | SRR7774320 | SRX4629504 | SAMN09934550 | Trinidad | 18442 |
SLC_4 | SLC 4 | SRR7774321 | SRX4629503 | SAMN09934551 | Trinidad | Tc17513 |
SNA0707 | SNA 707 | SRR7774322 | SRX4629502 | SAMN09934552 | Costa Rica | - |
sp1 | SP 1 [VEN] | SRR7774279 | SRX4629545 | SAMN09934583 | Venezuela (gDNA USDA) | - |
SPA_7 | SPA 7 [COL] | SRR7774323 | SRX4629501 | SAMN09934553 | Costa Rica | - |
SPEC_194_75 | SPEC 194 /75 | SRR7774324 | SRX4629500 | SAMN09934554 | Trinidad | Tc18235 |
SPEC_54_1 | SPEC 54 /1 | SRR7774325 | SRX4629499 | SAMN09934555 | Costa Rica | Tc05194 |
T675_A645_A1 | A 645 [ECU] | SRR7774341 | SRX4629483 | SAMN09934556 | Ecuador | - |
T678_B60_A1 | B 60 [ECU] | SRR7774340 | SRX4629484 | SAMN09934557 | Ecuador | - |
T684_EET233_A1 | EET 233 [ECU] | SRR7774337 | SRX4629487 | SAMN09934560 | Ecuador | - |
T685_EET387_A1 | EET 387 [ECU] | SRR7774336 | SRX4629488 | SAMN09934561 | Ecuador | - |
T686_LCT-368_A1 | LCT EEN 368 | SRR7774335 | SRX4629489 | SAMN09934562 | Ecuador | - |
T695_SCA-6_A1 | SCA 6 | SRR7774334 | SRX4629490 | SAMN09934563 | Ecuador | - |
TAP10_G12_A1 | TAP 10 [CHA] | SRR7774333 | SRX4629491 | SAMN09934564 | Ecuador | - |
TAP3_G70_A2 | TAP 3 [CHA] | SRR7774332 | SRX4629492 | SAMN09934565 | Ecuador | - |
TAP6_G12_A1 | TAP 6 [CHA] | SRR7774252 | SRX4629572 | SAMN09934566 | Ecuador | - |
TIP-1_G41_A1 | TIPUTINI 1 [CHA] | SRR7774253 | SRX4629571 | SAMN09934567 | Ecuador | - |
TRD_45 | TRD 45 | SRR7774191 | SRX4629633 | SAMN09934569 | Trinidad | 18443 |
TRD86 | TRD 86 | SRR7774188 | SRX4629636 | SAMN09934568 | Trinidad | - |
TSA654Zymo | TSA 654 | SRR7774248 | SRX4629576 | SAMN09934570 | Costa Rica | 17457 |
TSH1188 | TSH 1188 | SRR7774249 | SRX4629575 | SAMN09934571 | Brazil, MARS | - |
TSH516 | TSH 516 | SRR7774246 | SRX4629578 | SAMN09934572 | Costa Rica | 17455 |
UF_11 | UF 11 | SRR7774282 | SRX4629542 | SAMN09934576 | Costa Rica | 18446 |
UF_668 | UF 668 | SRR7774281 | SRX4629543 | SAMN09934577 | Costa Rica | 17456 |
UF_676 | UF 676 | SRR7774284 | SRX4629540 | SAMN09934578 | Costa Rica | Tc13037 |
UF12 | UF 12 | SRR7774247 | SRX4629577 | SAMN09934573 | Costa Rica | 17434 |
UF273_T1 | UF 273 | SRR7774244 | SRX4629580 | SAMN09934574 | Costa Rica | - |
UF273_T2 | UF 273 | SRR7774245 | SRX4629579 | SAMN09934575 | Costa Rica | - |
UNAP2_G78_A2 | UNAP 2 [CHA] | SRR7774283 | SRX4629541 | SAMN09934579 | Ecuador | - |