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Supplemental Material SUPPLEMENTAL MATERIAL THE LIST OF SUPPLEMENTAL FIGURES Supplemental Figure 1. The distribution of intervals between SNPs/indels and correlation of SNP and small indel densities. Supplemental Figure 2. Enriched GO groups in genes with 10 or more nonsynonymous SNPs. Supplemental Figure 3. Genes affected by small or large indels. Supplemental Figure 4. The detection of indels using Illumina paired-end reads and verification by PCR. Supplemental Figure 5. CNVs verification of three transposon groups by using sequencing reads densities. Supplemental Figure 6. Tetrad analysis for identification of meiotic CO and NCO. Supplemental Figure 7. A schematic illustration for detecting meiotic recombination using Illumina sequencing reads. Supplemental Figure 8. The positions of two detected COs on chromosome 4 in this study among the high CO rates regions reported by Drouaud et al. (Drouaud et al. 2006). Supplemental Figure 9. The Ler deletion located inside the 1st meiosis CO-4 was replaced by Col DNA sequence after meiotic recombination. Supplemental Figure 10. Meiosis turns genomic transposition into copy number variations. THE LIST OF SUPPLEMENTAL TABLES Supplemental Table 1. Summary of read number and coverage. Supplemental Table 2. The list of genes containing 10 or more nonsynonymous SNPs, nonsense SNPs, and potentially extended transcripts in Ler. Supplemental Table 3. Unknown genes and genetic variations. 1 Supplemental Table 4. Expression of genes with 10 or more nonsynonymous mutation and genes with nonsense mutation based on plant ontology. Supplemental Table 5. The list of 50 genes with dN/dS >1. Supplemental Table 6. The lists of genes affected by frameshift and nonframeshift small indels. Supplemental Table 7. The list of 1,615 large deletions and 700 large insertions in Ler genome. Supplemental Table 8. The list of 130 genes with full CDS deleted in the Ler genome. Supplemental Table 9. The list of 186 genes with partially deleted in the Ler genome. Supplemental Table 10. Gene duplication followed by reciprocal loss between Col and Ler. Supplemental Table 11. The list of meiotic crossovers detected in the two meioses. Supplemental Table 12. The list of gene conversions detected in the two meioses. Supplemental Table 13. Redistribution of SNPs and indels by crossing over meiotic crossovers and independent chromosome assortment. Supplemental Table 14. The locations of genetic structure variations between Col and Ler resulting in CNVs in two meiotic offspring. Supplemental Table 15. Gene families enriched for genomic variations. Supplemental Table 16. Correlation of genome size and genetic distance among various species. Supplemental Table 17. The list of primers used for PCR-based verification of some predicted indels between Col and Ler. Supplemental Table 18. The list of primers for PCR-based verification of predicted COs and NCOs. 2 A B Fraction Fraction 0 0.05 0.10 0.15 0.20 0.25 0.30 0 0.05 0.10 0.15 0.20 0.25 0.30 1 25 210 215 219 1 25 210 215 219 SNP interval (bp) Indel interval (bp) C 1000 100 10 1 1000 100 10 1 1000 100 10 1 1000 100 10 1 D E F 6 6 6 4 4 4 SNP indel indel 2 2 2 R 2 = 0.52 R 2 = 0.064 R 2 = 0.026 0 0 0 0 1 2 3 4 5 0 2 4 6 8 0 0.1 0.2 0.3 0.4 0.5 0.6 Indel Coverage CD S Supplemental Figure 1. The distribution of intervals between SNPs/indels and correlation of SNP and small indel densities. (A, B) Histogram of interval between SNPs (A) or indels (B). The fraction of intervals in each length range was plotted. The curve shows the fraction from exponential distribution, as the length of intervals between SNPs/indels follows exponential distribution if SNPs/indels are randomly distributed across the genome. The actual distribution of interval length has heavier tail than exponential distribution. For either SNP o indel, the difference between actual distribution and exponential distribution is statistical different (Kolmogorov-Smirnov test, p < 10e-10) (C) Parallel change of SNP and small indel density on Chr2-5. The density was defined to be the number of SNPs/indels per 100 Kb. The blue curves represent SNP densities and the red curves for small indels. Blue and red vertical bars below show the locations of large deletions and insertions, respectively. (D) Linear regression of SNP and indel densities in 10 Kb sliding windows. (E, F) Linear regression of small indel densities with read coverage (E) or CDS fraction (F) in 100 Kb sliding window. SNP and indel densities are log2 transformed. Near zero R square value suggests read coverage or CDS fraction does not contribute much to the correlation. 2 3 A G O :0003674 B m olecular function G O :0005575 cellular com ponent G O :0060089 (1.66e-09) G O :0005488 (5.66e-05) m olecular transducer G O :0003824 binding activity catalytic activity 192/432 | 11258/37767 25/432 | 422/37767 G O :0005623 cell G O :0004871 (1.66e-09) G O :0016740 (0.00715) G O :0000166 (5.72e-10) G O :0001882 (1.82e-14) G O :0043167 (0.00741) G O :0019825 (0.0327) G O :0005515 (2.44e-12) signal transducer G O :0016787 transferase activity nucleotide binding nucleoside binding ion binding oxygen binding protein binding activity hydrolase activity 61/432 | 3321/37767 68/432 | 2267/37767 61/432 | 1465/37767 42/432 | 2087/37767 9/432 | 255/37767 88/432 | 2944/37767 25/432 | 422/37767 G O :0044464 cell part G O :0016772 (0.000164) G O :0016817 (6.3e-08) G O :0017076 (6.48e-12) G O :0001883 (1.82e-14) G O :0004872 (4.62e-12) G O :0032553 (1.16e-12) G O :0043169 (0.00741) transferase activity, hydrolase activity, purine nucleotide purine nucleoside receptor activity ribonucleotide binding cation binding transferring phosphorus-containing groups acting on acid anhydrides binding binding 21/432 | 212/37767 61/432 | 1631/37767 42/432 | 2087/37767 45/432 | 1887/37767 33/432 | 839/37767 61/432 | 1713/37767 61/432 | 1465/37767 G O :0016020 m em brane G O :0004888 (1.04e-13) G O :0016818 (6.3e-08) G O :0032555 (1.16e-12) G O :0030554 (1.82e-14) G O :0016301 (0.000271) G O :0046872 (0.0036) transm em brane receptor hydrolase activity, purine ribonucleotide adenyl nucleotide kinase activity m etal ion binding activity acting on acid anhydrides, in phosphorus-containing anhydrides binding binding 40/432 | 1641/37767 42/432 | 1997/37767 21/432 | 171/37767 33/432 | 837/37767 61/432 | 1631/37767 61/432 | 1465/37767 G O :0044425 m em brane part G O :0032559 (3.6e-15) G O :0046914 (0.000407) G O :0016462 (5.8e-08) adenyl ribonucleotide transition m etal pyrophosphatase activity binding ion binding 33/432 | 832/37767 G O :0031224 (0.0041) 61/432 | 1384/37767 39/432 | 1618/37767 intrinsic to most significant m em brane 24/432 | 806/37767 G O :0017111 (1.88e-08) G O :0005524 (3.6e-15) G O :0008270 (5.39e-05) nucleoside-triphosphatase activity A TP binding zinc ion binding not significant 33/432 | 792/37767 61/432 | 1377/37767 36/432 | 1299/37767 Supplemental Figure 2. Enriched GO groups in genes with 10 or more nonsynonymous SNPs. (A) Enriched groups of molecular function. (B) Enriched groups of cellular component. 4 A B C Gene Gene Gene 0 50 100 150 200 0 50 100 150 200 0 20 40 60 80 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 more 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 more 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 more dN/dS value dN/dS value dN/dS value D E F ●● ● ● 1.8 ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●● ●●● ●●● ●●● ● ●● ● ● ●● ●● ● ●● ● ●● ● ● ●●●●●●●● ●● ● ● ●●●● ● ● ●●●● ● ● ●●●● ●● ● ●● ●● ●●●●● ● ● ●● ●● ● ● ●●● ● ● ● ●●● ● ● ●●●●● ● ● ● ●●● ● ● ● ● ● ● ● ● ●●●●● ● ● ● ● ● ● ●●●● ● ● ● ●● ●● ● ● ● ● ● ● ● ●●●●● ●● ● ●● ●● ● ● Expression ● Expression ● Expression ● ●●● ●● ● ● ● ● ●●●● ● ● ● ● ● ●● ● ● ● ● ● ●●● ● ● ● ● ● er er ●● ● er ● ● ● ● ● ● ● ●●● ● ●● ●● ●● ● ●● ● L ● ● ● L L ● ● ● ●●● ●● ● ● ● ● ●● ● ●●● ● ● ● ●●●●● ● ●●● ● ● ● ● ● ● ● ●●●●●● ● ● ● ● ●● ●● ● ●● ● ● ●●● ● ● ● ● ● ●●●●●● ● ● ●● ● ● ●●●●● ● ● ● ●●●●● ● ●●●● ● ● ● ●●●●● ● ● ● ● ●●●●●●●● ● ●● ● ● ●●● ●●●●●●●● ● ● ● ●● ●●● ● ● ●●●●●●●●●●●●● ●●●●●● ● ●●● ● ● ●●●●●●●● ●●●● ●●●●●●●●● ●●●●●●●● ● ● ● ● ●●●●●●● ● ● ●● ● ●●●●●●●● ●● ●●●●●● ● ● ●●●●●●●●● ● ● ●●● ● ● ● ●●●●●●● ●● ● ●●●●● ● ● ●●●●● ●● ● ● ● 0.6 0.8 1.0●●●● 1.2 1.4 1.6 ●●●●● ●●●● ●●●●●● ● ● ● ● ● ●●●●●● ●● ●●●● ●●●● ● ● 0.6 0.8● 1.0●● 1.2 1.4 1.6 ●● ● ● ● ●●●● ●●●● ●● ● ●●● ●●● 0.6 0.8 1.0●●●●●● 1.2● ● 1.4 1.6 ● ● ●●●● 0.6 0.8 1.0 1.2 1.4 1.6 0.6 0.8 1.0 1.2 1.4 1.6 0.6 0.8 1.0 1.2 1.4 1.6 1.8 Col Expression Col Expression Col Expression G H I G O :0003674 G O :0005575 m olecular function G O :0003674 m olecular function cellular com ponent G O :0060089 G O :0005488 m olecular transducer binding activity G O :0005488 binding G O :0004871 G O :0001882 (0.0191) G O :0005623 G O :0000166 signal transducer nucleoside binding nucleotide binding cell activity 56/834 | 1465/37767 G O :0030528 (2.05e-09) G O :0003676 (0.000118) transcription regulator nucleic acid binding G O :0017076 (0.0432) G O :0001883 (0.0191) activity 101/459 | 4842/37767 G O :0004872 G O :0032553 purine nucleotide purine nucleoside 75/459 | 2417/37767 receptor activity ribonucleotide binding binding binding 60/834 | 1713/37767 56/834 | 1465/37767 G O :0044464 cell part G O :0004888 (0.0391) G O :0030554 (0.0191) G O :0003677 (1.38e-08) G O :0032555 transm em brane receptor adenyl nucleotide purine ribonucleotide D N A binding activity binding binding 12/834 | 171/37767 56/834 | 1465/37767 81/459 | 2892/37767 G O :0012505 (0.00236) G O :0032559 (0.0281) adenyl ribonucleotide G O :0003700 (2.24e-09) endom em brane system binding transcription factor 52/834 | 1384/37767 117/834 | 3416/37767 activity 69/459 | 2173/37767 G O :0005524
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