SupplementaryFig. S1.A long PCR scheme for retrieval of missing sequence corresponding to a breaking point in a presumed misassembled region at the end of a pseudomolecule.
SupplementaryFig. S2.Diversity along soybean chromosomes 1 to 20. The horizontal axes are Mbp coordinated along the Williams 82 reference genome and approximate centromere positions proposed by Schmutz et al. 2010 are denoted by the thick arrows. Shown for each chromosome are relationship between physical and genetic positions (cM, black line), and corresponding recombination rates (red line, cM/Mb) calculated from 100-kb sliding windows for the genomic regions between adjacent markers (top panel), numbers of genes per 100 kb (black line) and numbers of transposable elements (TE) per 100 kb (middle panel), and numbers of single nucleotide polymorphic (SNP) sites per 100 kb (left y axis) and percentages of shared SNPs of Hwangkeum per the number of SNPs for IT182832 (bottom panel). In the top panel, the discrepant regions between the genetic and sequence-based physical maps are denoted by discontinuities. In the bottom panel, green lines represent Williams 82K, blue lines IT182932, red lines Hwangkeum, and black lines % shared SNP.
SupplementaryFig. S3.Single nucleotide divergence between soybean variants. The approximate 3.2 million single nucleotide differences among three soybean accessions, which were identified by aligning short reads against the Williams 82 reference genome sequence, were classified into shared and unique variations. The overlapping regions represent variants shared between two variants or all variants.
SupplementaryTable S2. Distribution of diversity or polymorphism informative content (PIC) values from genotyping 258 indel markers onto a diverse set of 12 soybean variants
PIC value / Number of indel markers0.1531 / 138
0.2779 / 27
0.2918 / 5
0.3750 / 20
0.3775 / 3
0.4029 / 4
0.4449 / 22
0.4862 / 16
0.4866 / 5
0.5000 / 6
0.5418 / 4
0.5695 / 1
0.5696 / 2
0.6112 / 2
0.6528 / 1
0.7085 / 1
0.7502 / 1
SupplementaryTable S3. List of indel markers in marker intervals corresponding to putative introgression regions in Hwangkeum (Glycine max) from G. soja where more than half of indel markers polymorphic between Williams 82 (G. max) and IT182932 (G. soja) were shown to be monomorphic between Hwangkeum and IT182932
Indel marker in marker-sparse interval / Genome sequence position / Polymorphism or monomorphism between Hwangkeum and IT182932 / Forward primer / Reverse primer / Allele size in Williams 82GMES0924 to Satt631(Gm03: 1310955..2916475)
GSINDEL19600 / 1516234 / Polymorphism / GAATTGTATTCTGAAACAGC / CACTCAAATCCTACGTTTAC / 161
GSINDEL19661 / 1684062 / Monomorphism / TTTACTATGGCATGATTTCT / TTCACCTAGGTAATTTTGAA / 143
GSINDEL19680 / 1742470 / Monomorphism / TTACATTGTTCAATCCTACC / TTTTCTTCTTGCCTTTAGTA / 152
GSINDEL19728 / 1908133 / Monomorphism / GGATTTTTCAATTGATTTTA / TCATCTCTCTCCTAACAGAA / 115
GSINDEL19743 / 1942952 / Monomorphism / TGCATTCCAATACTATTACC / AGTGATTTATGCTTTTTCAC / 116
GSINDEL19792 / 2045321 / Polymorphism / GTACTTCCATTAAAACATGC / ATGCTTTTGTTGTTGATTAT / 243
GSINDEL19902 / 2324329 / Monomorphism / GTCCTCTGAACAATAAACTG / TACACCGATTCCTTTAAATA / 216
GSINDEL19990 / 2558325 / Polymorphism / AATGGTTCACAAAACTTAGA / TATCACAGAAGAAGAGGCTA / 248
Satt316 to Sca-364a (Gm06: 47485161..48661496)
GSINDEL56203 / 47572099 / Monomorphism / AAATAAGCAATAGGCACTAA / GTTTTTAATTATGAGGCAAA / 130
GSINDEL56300 / 47798156 / Monomorphism / ATACGTGGCAATAGTATGAT / CAAGATTTTGAGTTAAGGTG / 122
GSINDEL56311 / 47820269 / Monomorphism / TGAGAAATCGTTTATTTCAT / CTTTGTTTTTCTTAAGGTGA / 179
GSINDEL56321 / 47837905 / Polymorphism / CTTGTTTTTGTTGATTCTTC / TTAACCTATTTTCTGTCCAA / 200
GSINDEL56371 / 47956076 / Monomorphism / TATTTCTTTTGAAACAGACC / TACTCTTCCCTTTGTCATTA / 180
GSINDEL56385 / 47986268 / Monomorphism / GAATAAGAAAGAGAGGAAGC / TAGGGGAAAATGAAGACTA / 177
GSINDEL56400 / 48014768 / Monomorphism / ATACATTTCATTTCATCCAG / AAGTTTCACGTCAGTTAAAA / 160
GSINDEL56414 / 48074822 / Monomorphism / TGACAACTAAAATGACAATAAA / CATTTGACATTGCTATTATG / 132
GSINDEL56439 / 48178039 / Monomorphism / GATCCAACTTACCATAATCA / TCAAAAATAAAATGGAGTGT / 198
GSINDEL56531 / 48415540 / Polymorphism / TCTTCAATTCCGAATACTAA / ATATATCAACGAAATGCTTC / 161
GMES1600 to GMES6736 (Gm09: 39751797..41849066)
GSINDEL84893 / 40031613 / Polymorphism / CAATTTTTAAACAAGCTCAA / AGTCTTTTCATGTTATGCAC / 195
GSINDEL85007 / 40364072 / Monomorphism / ACCAGCAACACATTATTTAT / TGCTGAACTGTCTTCTACTT / 210
GSINDEL85023 / 40412092 / Monomorphism / GTAACACGACACAAACTTCT / GAACAAAATGAAAATATGCT / 163
GSINDEL85030 / 40419277 / Monomorphism / GAATGAATGAATGTTTGTTT / GGTAGTGAATTACAACCAAG / 130
GSINDEL85048 / 40498520 / Polymorphism / GTAAGGACTAAGGATAAAGC / CTTTCAAGCTGGATTTGAC / 204
GSINDEL85121 / 40623731 / Monomorphism / ACTGTGTTGTTAGCATTTTT / CCAACTCGTCAACTCTATT / 187
GSINDEL85147 / 40673473 / Monomorphism / AAAGAGTTGCATTACAAGAG / CTTCCCTTTTCTTCTTTTAT / 134
GSINDEL85155 / 40694764 / Monomorphism / TGCCATATCTTATCTTTTGT / GGACTGTGTACTTGATAGGA / 141
GSINDEL85193 / 40763413 / Monomorphism / GACTCTTCTTCTGTCTCCTC / TTTTAATTGGGTGAGAGTAA / 169
GSINDEL85269 / 41096510 / Monomorphism / TATGCTCGTACTGAGATTTT / GAGAGTGATCCATTCAAAG / 232
GSINDEL85271 / 41103592 / Monomorphism / ACTCAGGAGATTCTTGAAAT / GCTAGTCAATTGGAAACAT / 134
GSINDEL85272 / 41109897 / Monomorphism / TATACACCGAGCTTAATAGG / AAGACCTTCAGTACAGTTCA / 137
GSINDEL85282 / 41140003 / Monomorphism / ATTTACCATGAGCAGATTTA / CTTGGTCCAATCTTAGTGT / 232
GSINDEL85324 / 41280723 / Monomorphism / GTGCCACTTATGTGAGATAC / AAAAACTTTGATATTGTGGA / 130
GSINDEL85332 / 41294386 / Polymorphism / TATACACAAAGTTGCACAAA / ATGTCACTCAAAATAGATGC / 179
GSINDEL85333 / 41295818 / Monomorphism / GAGGGGATATCTGTGTATCT / CTTCACTTGGTGATAGAGAA / 244
GSINDEL85335 / 41297158 / Polymorphism / ACGTGAAAAGTGTCTCTAAA / TTCATCTTCTCCTTTTCATA / 216
GSINDEL85359 / 41384266 / Monomorphism / ATTGAAGAGTCCTCTACCTC / GTAGCTAGCATTTCAAGAAG / 183
GSINDEL85435 / 41537237 / Polymorphism / CCCATGACTCTTATCTCATA / GATACTTGGGAAGAGAAAGT / 229
A203.p1to Sca_189b (Gm15: 7469277..8817679)
GSINDEL136839 / 7777973 / Monomorphism / AAAAGAGTGCATAATGATTT / ATTTCCAAGATTTTTCTTTT / 117
GSINDEL136934 / 8075682 / Polymorphism / TCTCAAAATAAAAATGGAAG / TTATCAAATAACAAGGGAAT / 131
GSINDEL136982 / 8167899 / Monomorphism / ACAAATCCAGCAAACTATA / CTTAGGAAATTCATTTGATG / 156
GSINDEL137010 / 8288840 / Polymorphism / CTTTGCAAAATAAGTTTAGG / CTTTTTCTCTCAATTTTTCA / 195
GSINDEL137069 / 8507084 / Monomorphism / TGGAATTTTCTGAAATAAAG / TAATCTCAAGAGGAGATGAA / 174
GSINDEL137071 / 8509641 / Monomorphism / TTTAGATAACCTTCCTCACA / TTCACAGTAGGTTAGACGTT / 171
GSINDEL137103 / 8609958 / Polymorphism / CATAAGGGAGGGTAATACTT / TTAATTGATCCATGTTCATC / 133
GSINDEL137141 / 8721390 / Monomorphism / TTGGTGGTATCACTAACTTT / ATTTAGGCTTAGGGTCTAAC / 141
SupplementaryTable S4. List of primer sets for long PCR amplification of breaking points of discrepant segments between the current genetic map and Williams 82 genome sequence assembly (Glyma1) and GenBank accession numbers of sequences of the retrieved sequences
Discrepant segment / Primer set / Forward primer sequence / Reverse primer sequence / GenBank accession numberChr 5 / Chr5A1 / gcaacgtttgtcttcgttca / Gttaatctcgccggaaaattg / JQ924190
Chr 11 / JQ924191
BE020413-containing 5’ end / BE020413 / AGTTAAGATATGTTGCTTGG / AGTGTTTGTTGTATGGTTGT
3’ end / Chr11B1 (primary PCR) / GGCCACTTCTGGAATCGTAA / GCCCCACTGGAAGTATTTGA
Chr11B1-2 (nested PCR) / GACTCGGTGACACCATAAGT / GTGAATTGTGTACGGGTTTT
Chr 14 / Chr14B2 / GAACATATATGGGGTGCATGA / CATTCTACGCTAGAAGCTGAA / JQ924192
Insertion site of unplaced scaffold_41 on Chr 17
Upper / Scaffold41-be / ATATGCCACCCAAATAAAAA / GTTTGGGTGAAAAACAAGAG / JQ924193
Lower / Scaffold41-end / CCAGACAAAAGAGAAAGTGG / GGAAGGACAAGGGTTATTTT / JQ924194
Chr 19 / Chr19L / GAAGGATACAAGTGAAAAAGTACAA / GATGTAGACAACATATCCCCTTC / JQ924195
SupplementaryTable S5. Summary of mapping by chromosome
Chromosome number / Number of markers / Distance (cM) / cM/marker / Physical length (Mb) / kb/marker / Recombination rate (cM/Mb)1 / 128 / 107.9 / 0.8 / 55.9 / 436.7 / 1.9
2 / 113 / 138.6 / 1.2 / 51.7 / 457.5 / 2.7
3 / 67 / 113.2 / 1.7 / 47.8 / 713.4 / 2.4
4 / 59 / 105.7 / 1.8 / 49.2 / 833.9 / 2.1
5 / 79 / 110.0 / 1.4 / 41.9 / 530.4 / 2.6
6 / 74 / 125.1 / 1.7 / 50.7 / 685.1 / 2.5
7 / 64 / 114.9 / 1.8 / 44.6 / 696.9 / 2.6
8 / 93 / 155.3 / 1.7 / 47.0 / 505.4 / 3.3
9 / 73 / 109.4 / 1.5 / 46.8 / 641.1 / 2.3
10 / 80 / 142.6 / 1.8 / 51.0 / 637.5 / 2.8
11 / 76 / 133.0 / 1.8 / 39.2 / 515.8 / 3.4
12 / 72 / 106.1 / 1.5 / 40.1 / 556.9 / 2.6
13 / 110 / 115.3 / 1.0 / 44.4 / 403.6 / 2.6
14 / 76 / 113.4 / 1.5 / 49.7 / 653.9 / 2.3
15 / 78 / 124.9 / 1.6 / 50.9 / 652.6 / 2.5
16 / 65 / 91.9 / 1.4 / 37.4 / 575.4 / 2.5
17 / 64 / 119.2 / 1.9 / 41.9 / 654.7 / 2.8
18 / 73 / 116.8 / 1.6 / 62.3 / 853.4 / 1.9
19 / 75 / 112.0 / 1.5 / 50.6 / 674.7 / 2.2
20 / 62 / 105.9 / 1.7 / 46.8 / 754.8 / 2.3
Total/average / 1581 / 2361.2 / 1.5 / 950.0 / 600.9 / 2.5
SupplementaryTable S6. Comparison of recombination rate of plants with sequenced genomes
Species name (common name) / Predicted genome size (Mb) / Number of chromosomes / Sequenced genome size (Mb) / Transposable element (TE) content (%) / Sequenced genome size excluding TE / Genetic map length (cM) / Recombination rate (cM/Mb)a / Adjusted recombination rate (cM/Mb)b / ReferencesdArabidopsis thaliana / 125 / 5 / 119 / 16 / 102 / 597 / 5.0 / 5.9 / 1, 2, 3
Arabidopsis lyrata / 230 / 8 / 207 / 23 / 159 / 515 / 2.5 / 3.2 / 2, 4, 5
Fragariavesca (strawberry) / 240 / 7 / 210 / 22 / 164 / 559 / 2.7 / 3.4 / 6
Brachypodiumdistachyon / 355 / 5 / 272 / 26 / 201 / 1598 / 5.9 / 8 / 7, 8
Brassica rapa(pakchoi) / 485 / 10 / 284 / 40 / 170 / 1123 / 4.0 / 6.6 / 9, 10
Medicagotruncatula / 454 / 8 / 375 / 30 / 263 / 567 / 1.5 / 2.2 / 11, 12
Oryza sativa (rice) / 405 / 12 / 389 / 35 / 264 / 1530 / 3.9 / 5.8 / 13, 14
Solanumtuberosum (potato) / 844 / 12 / 727 / 62 / 276 / 762c / 1.1 / 2.8 / 15, 16
Sorghum bicolor (sorghum) / 748 / 10 / 730 / 62 / 277 / 1059 / 1.5 / 3.8 / 17, 18
Glycine max (soybean) / 1115 / 20 / 937 / 57 / 402 / 2361 / 2.5 / 5.9 / 19,
this study
Zea mays (maize) / 2300 / 10 / 2300 / 85 / 345 / 2349 / 1.0 / 6.8 / 20, 21
aCalculated by dividing the map length by the sequenced genome size. We presume that, as the sequenced genomes of rice and Arabidopsis demonstrated tendency of overestimating genome size by flow cytometry [Arabidopsis Genome Initiative (2000); International Rice Genome Sequencing Project (2005)], the sequenced genome sizes are more accurate than the predicted genome sizes.
bCalculated by dividing the map length by the sequenced genome size excluding TE.
cAverage genetic length of 751 cM for the maternal map and 773 cM for the paternal map.
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SupplementaryTable S7. Summary of sequencing and variations for three soybean varieties
VarietyCategory / IT182932 / Hwangkeum / Williams 82
Mapping
Total bases / 36,880,852,541 / 19,983,900,227 / 16,544,562,819
Mean depth / 38.82 / 21.03 / 17.41
Coveragea
%_bases_above_1 / 97.4 / 97.4 / 98.5
%_bases_above_5 / 93.2 / 95.9 / 97.6
%_bases_above_10 / 85.5 / 92.0 / 89.8
%_bases_above_20 / 69.2 / 56.2 / 34.2
SNP
Total / 2,397,205 / 1,236,277 / 113,587
Known / 1,365,216 / 817,605 / 44,566
Homozygous / 2,286,168 / 1,165,945 / 51,454
Heterozygous / 111,037 / 70,332 / 62,133
Transition / 1,575,531 / 785,647 / 63,381
Transversion / 821,674 / 450,630 / 50,206
Exon / 116,121 / 55,029 / 5,610
Exon known / 73,935 / 41,882 / 2,008
Exon novel / 42,186 / 13,147 / 3,602
Exon homozygous / 108,819 / 50,081 / 2,268
Exon heterozygous / 7,302 / 4,948 / 3,342
Exon transition / 68,941 / 32,637 / 3,081
Exon transversion / 47,180 / 22,392 / 2,529
CDS / 85,330 / 40,543 / 4,388
5’ UTR / 9,706 / 4,420 / 423
3’ UTR / 21,886 / 10,468 / 856
Intron / 236,471 / 115,952 / 9,295
Silent / 38,587 / 18,489 / 1,932
Missense / 45,798 / 21,624 / 2,401
Nonsense / 896 / 414 / 50
Readthrough / 131 / 65 / 9
Splice_site / 701 / 357 / 50
Start_codon / 162 / 68 / 10
Indel
Total / 302,013 / 236,276 / 29,105
Homozygous / 286,097 / 224,203 / 20,269
Heterozygous / 15,916 / 12,073 / 8,836
Tandem_repeat / 213,098 / 173,403 / 22,621
Exon / 14,072 / 7,127 / 1,162
Exon novel / 14,072 / 7,127 / 1,162
Exon homozygous / 13,191 / 6,714 / 930
Exon heterozygous / 881 / 413 / 232
Exon tandem_repeat / 9,885 / 5,171 / 917
CDS / 4,879 / 2,452 / 655
5’ UTR / 3,476 / 1,633 / 199
3’ UTR / 5,775 / 3,073 / 316
Intron / 47,994 / 28,876 / 3,285
Frameshift / 2,772 / 1,531 / 595
Inframe / 2,107 / 921 / 60
Splice_site / 264 / 139 / 31
Start_codon / 85 / 41 / 5
aPercentageof the Williams 82 reference genome sequence covered with short reads higher than 1, 5, 10, and 20