Table 2 Open in new tab Comparison of...

	Cultivar	Criollo V2	Matina 1–6	Pound7
Contiguity	Total length (bp)	306,380,296	330,821,837	392,822,621	393,460,530	388,496,692	379,301,597	379,301,597	390,893,205	341,510,689	345,320,506	345,043,684	344,633,077	344,633,077	345,527,408
N. contigs	7743	20,103	1038	1038	1834	1506	1517	2720	663	663	776	730	769	813
Longest contig (bp)	936,847	1,030,196	4,922,249	4,933,427	4,932,277	4,932,277	4,932,277	4,932,277	9,646,223	9,762,425	8,557,809	8,557,809	8,557,809	9,762,425
Shortest contig (bp)	1004	150	2223	2220	1001	1001	619	619	9898	10,028	1009	1032	627	627
Median contig length (bp)	17,900	1,369	151,556	151,878	65,356	88,375	88,602	5518	166,639	166,970	134,792	155,726	146,729	107,747
N50 (bp)	87,439	84,396	906,913	907,755	769,569	803,644	781,587	757,789	1,402,148	1,425,322	1,284,321	1,284,321	1,256,900	1,326,996
N90 (bp)	18,795	14,971	140,537	140,664	127,828	142,289	142,272	122,633	276,232	280,231	262,563	265,332	250,503	253,804
N95 (bp)	11,288	5318	97,563	97,802	81,742	94,211	94,211	76,298	130,841	132,654	126,970	131,288	118,665	118,665
L50	879	1080	124	124	142	136	138	145	66	66	74	74	78	70
L90	3776	4380	550	551	627	570	576	651	282	282	300	299	313	299
L95	4810	6190	719	719	816	732	738	851	374	374	396	393	413	398
% GC	34.09%	34.01%	34.03%	33.84%	33.86%	33.87%	33.87%	33.85%	33.79%	33.96%	33.96%	33.96%	33.96%	33.96%
BUSCO v3	Complete, total (%)	95.14%	95.83%	62.57%	95.49%				95.21%	54.38%	95.35%				95.28%
Complete, total (N)	1370	1380	901	1375				1371	783	1373				1372
Complete, single copy	1350	1356	875	1335				1325	772	1346				1342
Complete, duplicated	20	24	26	40				46	11	27				30
Fragmented	24	22	103	22				21	112	23				23
Missing	46	38	436	43				48	545	44				45

Cultivar

Criollo V2

Matina 1–6

Pound7

Assembly data/method

PacBio RSI, 454, Illumina, Sanger of BACs

454, Illumina, Sanger of BACs

minimap–miniasm–racon

Canu-SMARTde novo

Version/stage

v2.0

v1.1

Unpolished

Polished

Split (by coverage)

Nonredundant

Split (by map consensus)

Final draft

Unpolished

Polished

Split (by coverage)

Nonredundant

Split (by map consensus)

Final draft

Contiguity

Total length (bp)

306,380,296

330,821,837

392,822,621

393,460,530

388,496,692

379,301,597

390,893,205

341,510,689

345,320,506

345,043,684

344,633,077

345,527,408

N. contigs

7743

20,103

1038

1834

1506

1517

2720

663

776

730

769

813

Longest contig (bp)

936,847

1,030,196

4,922,249

4,933,427

4,932,277

9,646,223

9,762,425

8,557,809

9,762,425

Shortest contig (bp)

1004

150

2223

2220

1001

619

9898

10,028

1009

1032

627

Median contig length (bp)

17,900

1,369

151,556

151,878

65,356

88,375

88,602

5518

166,639

166,970

134,792

155,726

146,729

107,747

N50 (bp)

87,439

84,396

906,913

907,755

769,569

803,644

781,587

757,789

1,402,148

1,425,322

1,284,321

1,256,900

1,326,996

N90 (bp)

18,795

14,971

140,537

140,664

127,828

142,289

142,272

122,633

276,232

280,231

262,563

265,332

250,503

253,804

N95 (bp)

11,288

5318

97,563

97,802

81,742

94,211

76,298

130,841

132,654

126,970

131,288

118,665

L50

879

1080

124

142

136

138

145

L90

3776

4380

550

551

627

570

576

651

282

300

299

313

299

L95

4810

6190

719

816

732

738

851

374

396

393

413

398

% GC

34.09%

34.01%

34.03%

33.84%

33.86%

33.87%

33.85%

33.79%

33.96%

BUSCO v3

Complete, total (%)

95.14%

95.83%

62.57%

95.49%

95.21%

54.38%

95.35%

95.28%

Complete, total (N)

1370

1380

901

1375

1371

783

1373

1372

Complete, single copy

1350

1356

875

1335

1325

772

1346

1342

Complete, duplicated

Fragmented

103

112

Missing

436

545

	Cultivar	Criollo V2	Matina 1–6	Pound7
Contiguity	Total length (bp)	306,380,296	330,821,837	392,822,621	393,460,530	388,496,692	379,301,597	379,301,597	390,893,205	341,510,689	345,320,506	345,043,684	344,633,077	344,633,077	345,527,408
N. contigs	7743	20,103	1038	1038	1834	1506	1517	2720	663	663	776	730	769	813
Longest contig (bp)	936,847	1,030,196	4,922,249	4,933,427	4,932,277	4,932,277	4,932,277	4,932,277	9,646,223	9,762,425	8,557,809	8,557,809	8,557,809	9,762,425
Shortest contig (bp)	1004	150	2223	2220	1001	1001	619	619	9898	10,028	1009	1032	627	627
Median contig length (bp)	17,900	1,369	151,556	151,878	65,356	88,375	88,602	5518	166,639	166,970	134,792	155,726	146,729	107,747
N50 (bp)	87,439	84,396	906,913	907,755	769,569	803,644	781,587	757,789	1,402,148	1,425,322	1,284,321	1,284,321	1,256,900	1,326,996
N90 (bp)	18,795	14,971	140,537	140,664	127,828	142,289	142,272	122,633	276,232	280,231	262,563	265,332	250,503	253,804
N95 (bp)	11,288	5318	97,563	97,802	81,742	94,211	94,211	76,298	130,841	132,654	126,970	131,288	118,665	118,665
L50	879	1080	124	124	142	136	138	145	66	66	74	74	78	70
L90	3776	4380	550	551	627	570	576	651	282	282	300	299	313	299
L95	4810	6190	719	719	816	732	738	851	374	374	396	393	413	398
% GC	34.09%	34.01%	34.03%	33.84%	33.86%	33.87%	33.87%	33.85%	33.79%	33.96%	33.96%	33.96%	33.96%	33.96%
BUSCO v3	Complete, total (%)	95.14%	95.83%	62.57%	95.49%				95.21%	54.38%	95.35%				95.28%
Complete, total (N)	1370	1380	901	1375				1371	783	1373				1372
Complete, single copy	1350	1356	875	1335				1325	772	1346				1342
Complete, duplicated	20	24	26	40				46	11	27				30
Fragmented	24	22	103	22				21	112	23				23
Missing	46	38	436	43				48	545	44				45

Table 2

Open in new tab

Comparison of cacao genome assemblies

	Cultivar	Criollo V2	Matina 1–6	Pound7
	Assembly data/method	PacBio RSI, 454, Illumina, Sanger of BACs	454, Illumina, Sanger of BACs	minimap–miniasm–racon						Canu-SMARTde novo
	Version/stage	v2.0	v1.1	Unpolished	Polished	Split (by coverage)	Nonredundant	Split (by map consensus)	Final draft	Unpolished	Polished	Split (by coverage)	Nonredundant	Split (by map consensus)	Final draft
Contiguity	Total length (bp)	306,380,296	330,821,837	392,822,621	393,460,530	388,496,692	379,301,597	379,301,597	390,893,205	341,510,689	345,320,506	345,043,684	344,633,077	344,633,077	345,527,408
	N. contigs	7743	20,103	1038	1038	1834	1506	1517	2720	663	663	776	730	769	813
	Longest contig (bp)	936,847	1,030,196	4,922,249	4,933,427	4,932,277	4,932,277	4,932,277	4,932,277	9,646,223	9,762,425	8,557,809	8,557,809	8,557,809	9,762,425
	Shortest contig (bp)	1004	150	2223	2220	1001	1001	619	619	9898	10,028	1009	1032	627	627
	Median contig length (bp)	17,900	1,369	151,556	151,878	65,356	88,375	88,602	5518	166,639	166,970	134,792	155,726	146,729	107,747
	N50 (bp)	87,439	84,396	906,913	907,755	769,569	803,644	781,587	757,789	1,402,148	1,425,322	1,284,321	1,284,321	1,256,900	1,326,996
	N90 (bp)	18,795	14,971	140,537	140,664	127,828	142,289	142,272	122,633	276,232	280,231	262,563	265,332	250,503	253,804
	N95 (bp)	11,288	5318	97,563	97,802	81,742	94,211	94,211	76,298	130,841	132,654	126,970	131,288	118,665	118,665
	L50	879	1080	124	124	142	136	138	145	66	66	74	74	78	70
	L90	3776	4380	550	551	627	570	576	651	282	282	300	299	313	299
	L95	4810	6190	719	719	816	732	738	851	374	374	396	393	413	398
	% GC	34.09%	34.01%	34.03%	33.84%	33.86%	33.87%	33.87%	33.85%	33.79%	33.96%	33.96%	33.96%	33.96%	33.96%
BUSCO v3	Complete, total (%)	95.14%	95.83%	62.57%	95.49%				95.21%	54.38%	95.35%				95.28%
	Complete, total (N)	1370	1380	901	1375				1371	783	1373				1372
	Complete, single copy	1350	1356	875	1335				1325	772	1346				1342
	Complete, duplicated	20	24	26	40				46	11	27				30
	Fragmented	24	22	103	22				21	112	23				23
	Missing	46	38	436	43				48	545	44				45

	Cultivar	Criollo V2	Matina 1–6	Pound7
	Assembly data/method	PacBio RSI, 454, Illumina, Sanger of BACs	454, Illumina, Sanger of BACs	minimap–miniasm–racon						Canu-SMARTde novo
	Version/stage	v2.0	v1.1	Unpolished	Polished	Split (by coverage)	Nonredundant	Split (by map consensus)	Final draft	Unpolished	Polished	Split (by coverage)	Nonredundant	Split (by map consensus)	Final draft
Contiguity	Total length (bp)	306,380,296	330,821,837	392,822,621	393,460,530	388,496,692	379,301,597	379,301,597	390,893,205	341,510,689	345,320,506	345,043,684	344,633,077	344,633,077	345,527,408
	N. contigs	7743	20,103	1038	1038	1834	1506	1517	2720	663	663	776	730	769	813
	Longest contig (bp)	936,847	1,030,196	4,922,249	4,933,427	4,932,277	4,932,277	4,932,277	4,932,277	9,646,223	9,762,425	8,557,809	8,557,809	8,557,809	9,762,425
	Shortest contig (bp)	1004	150	2223	2220	1001	1001	619	619	9898	10,028	1009	1032	627	627
	Median contig length (bp)	17,900	1,369	151,556	151,878	65,356	88,375	88,602	5518	166,639	166,970	134,792	155,726	146,729	107,747
	N50 (bp)	87,439	84,396	906,913	907,755	769,569	803,644	781,587	757,789	1,402,148	1,425,322	1,284,321	1,284,321	1,256,900	1,326,996
	N90 (bp)	18,795	14,971	140,537	140,664	127,828	142,289	142,272	122,633	276,232	280,231	262,563	265,332	250,503	253,804
	N95 (bp)	11,288	5318	97,563	97,802	81,742	94,211	94,211	76,298	130,841	132,654	126,970	131,288	118,665	118,665
	L50	879	1080	124	124	142	136	138	145	66	66	74	74	78	70
	L90	3776	4380	550	551	627	570	576	651	282	282	300	299	313	299
	L95	4810	6190	719	719	816	732	738	851	374	374	396	393	413	398
	% GC	34.09%	34.01%	34.03%	33.84%	33.86%	33.87%	33.87%	33.85%	33.79%	33.96%	33.96%	33.96%	33.96%	33.96%
BUSCO v3	Complete, total (%)	95.14%	95.83%	62.57%	95.49%				95.21%	54.38%	95.35%				95.28%
	Complete, total (N)	1370	1380	901	1375				1371	783	1373				1372
	Complete, single copy	1350	1356	875	1335				1325	772	1346				1342
	Complete, duplicated	20	24	26	40				46	11	27				30
	Fragmented	24	22	103	22				21	112	23				23
	Missing	46	38	436	43				48	545	44				45

Table of contig statistics for both reference genomes, and for each stage of (both) assemblies of Pound 7. For each Pound 7 assembly, the stages are listed in the left-to-right order starting with the “uncorrected” assembly and ending with the “final draft” set of contigs. Splitting steps were checked to make sure that they did not partially intersect BUSCO hits. Note: BUSCO summaries for both “final draft” assemblies were run using v3.0.2, on a different computer.

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