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Fig. S1. Genome Alignment of Rufipogon, Indica and Japonica Against O

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Fig. S1. Genome Alignment of Rufipogon, Indica and Japonica Against O ) ) ) 3 8 7 6 9 9 H 4 S Z R M ( ( ( a a a c c c i i i d d d n n n i i i ) ) P 4 S G ) G E 8 R H I R ( ( I ( a a a c c indica accessions. performed using MUMmer. A large inversion, marked using Fig. S1. i i c i n n d o o n p p i a a j j Genome alignment of rufipogon, indica and japonica against ) ) ) 3 o m 4 p o 9 t p 1 i i H N W ( ( ( a a n c c i i o n g n o o o p p p i a a f j j u r O. longistaminata a blue circle, was found in O. longistaminata Fig. S2. Breakpoint of the inversion in indica identified by genome alignment against O. longistaminata. Fig. S3. Venn diagrams based on (a) DEL, (b) DUP, and (c) INV detected from Illumina, PacBio, and Genome data. See Figure 1 for the results combined across the three SV categories. Fig. S4. Distribution of genetic diversity (π) for SNPs and SVs (DEL, DUP, TRA, INV) along chromosome 2 in rufipogon. Light blue bar represents the centromere. Fig. S5. Distribution of genetic diversity (π) for SNPs and SVs (DEL, DUP, TRA, INV) along chromosome 2 in indica. Light blue bar represent the centromere. Fig. S6. Distribution of genetic diversity (π) for SNPs and SVs (DEL, DUP, TRA, INV) along chromosome 2 in japonica. Light blue bar represents the centromere. Fig. S7. The correlation (r) between genetic diversity (π) of SVs and that of SNPs and indels in rufipogon (a), indica (b), and japonica (c). (a) (d) rufipogon Syn Gypsy CACTA Mutator hAT Mariner 0.6 Nsyn Copia LINE Helitron Harbinger SINE 0.2 n n 0.4 o o i i t t r r o o p p o 0.1 o r r P P 0.2 0.0 0.0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 < -10 (-10, -1) (-1, 0) (0, 1) > 1 (b) indica (e) 0.4 Syn Gypsy CACTA Mutator hAT Mariner Nsyn Copia LINE Helitron Harbinger SINE n o i 0.3 0.4 n t r o i o t p r o 0.2 o r p P o r 0.2 P 0.1 0.0 0.0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 < -10 (-10, -1) (-1, 0) (0, 1) > 1 (c) (f) 0.6 japonica Syn Gypsy CACTA Mutator hAT Mariner Nsyn Copia LINE Helitron Harbinger SINE n o i 0.4 0.4 t n r o o i t p r o o r p P o 0.2 r 0.2 P 0.0 0.0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 < -10 (-10, -1) (-1, 0) (0, 1) > 1 Derived allele frequency Fitness effects (NeS) (g) exon intron intergenic 1.00 y c 0.75 n e u 0.50 q e r F 0.25 0.00 y a r n r r s i TA E o o T e e E p p C IN t r A g n IN y o L a it h n ri S G C A t l i a C u e rb M H a M H Fig. S8. Graphs (a), (b) and (c) illustrate the SFS for various TE families in rufipogon, indica, japonica, respectively. Graphs (d), (e) and (f) represent the DFEs estimates for each taxon and each family. (g) The frequency of SVs within exons, introns and intergenic regions for TEs of various families within the Nipponbare reference. rufipogon indica japonica Additive Heterozygous Recessive s t n a i r a v f o r e b m u N Variant types Fig. S9. The additive, heterozygous and recessive (homozygous) burden for three taxa and various categories of SV. See Figure 4 of the main text to see the additive, heterozygous and recessive burden for all of SV. Fig. S10. Genomic differentiation (Dxy) between rufipogon and indica (a), rufipogon and japonica (b), and indica and japonica (c) based on SNPs and SVs in 20 kb windows. The dashed line represents the 99% cutoff. The arrows denote a couple of genes of interest. Fig. S11. Genomic differentiation (FST) between rufipogon and indica (a), rufipogon and japonica (b), and indica and japonica (c) based on SNPs and SVs in 20 kb non-overlapping windows. The dashed line represents the 99% cutoff. Arrows denote genes of interest. Fig. S12. Comparison of FST between SNPs and SVs. (a) FST is between rufipogon and indica, (b) FST is between rufipogon and japonica, (c) FST is between indica and japonica. The dashed line represents the 99% cutoff. Red dots represent the sites of significant differentiation in both SNP and SV, and there are 26, 12 and 10 sites in (a) FST between rufipogon and indica, (b) FST between rufipogon and japonica, (c) FST between indica and japonica, respectively. Fig. S13. Selective sweeps for rufipogon (a), indica (b) and japonica (c) detected by composite likelihood ratio (CLR) test based on SNPs and SVs in 20 kb non-overlapping windows. The dashed line represents the 99% cutoff. Red arrow represent a gene Ghd7 related to tillering. Fig. S14. Comparison of CLR between SNPs and SVs for (a) rufipogon, (b) indica and (c) japonica. These graphs reveal little correspondence (red dots) between CLRs based on SNPs (left) and SVs (right) in Figure S13. Table S1. List of the 46 mislabelled accessions. Run accession Origin Source1 Grouped in this study 1 ERR2245547 indica Zhao et al. 2018 rufipogon 2 ERR609561-ERR609580 indica Wang et al. 2018 temperate japonica 3 ERR617283-ERR617288 indica Wang et al. 2018 rufipogon 4 ERR619511-ERR619524 indica Wang et al. 2018 aus 5 ERR621557-ERR621569 indica Wang et al. 2018 rufipogon 6 ERR622337-ERR622356 indica Wang et al. 2018 aus 7 ERR625701-ERR625712 indica Wang et al. 2018 rufipogon 8 SRR3234369 indica Zhang et al. 2016a rufipogon 9 SRR5011847 indica Du et al. 2017 rufipogon 10 ERR2241054 temperate japonica Zhao et al. 2018 tropical japonica 11 ERR2245540 temperate japonica Zhao et al. 2018 tropical japonica 12 ERR615186-ERR615191 temperate japonica Wang et al. 2018 tropical japonica 13 ERR615877-ERR615882 temperate japonica Wang et al. 2018 tropical japonica 14 ERR626638-ERR626643 temperate japonica Wang et al. 2018 indica 15 ERR629716-ERR629721 temperate japonica Wang et al. 2018 indica 16 ERR629752-ERR629757 temperate japonica Wang et al. 2018 indica 17 ERR636841-ERR636846 temperate japonica Wang et al. 2018 temperate japonica 18 ERR637045-ERR637050 temperate japonica Wang et al. 2018 tropical japonica 19 ERR607669-ERR607674 tropical japonica Wang et al. 2018 temperate japonica 20 ERR608057-ERR608062 tropical japonica Wang et al. 2018 temperate japonica 21 ERR608413-ERR608426 tropical japonica Wang et al. 2018 indica 22 ERR611071-ERR611090 tropical japonica Wang et al. 2018 indica 23 ERR611151-ERR611170 tropical japonica Wang et al. 2018 indica 24 ERR611517-ERR611536 tropical japonica Wang et al. 2018 indica 25 ERR613946-ERR613959 tropical japonica Wang et al. 2018 aromatic 26 ERR616381-ERR616386 tropical japonica Wang et al. 2018 temperate japonica 27 ERR626504-ERR626509 tropical japonica Wang et al. 2018 indica 28 ERR629842-ERR629855 tropical japonica Wang et al. 2018 indica 29 ERR630772-ERR630791 tropical japonica Wang et al. 2018 indica 30 ERR630970-ERR630989 tropical japonica Wang et al. 2018 indica 31 ERR636847-ERR636852 tropical japonica Wang et al. 2018 temperate japonica 32 ERR2240123 rufipogon Zhao et al. 2018 aus 33 DRR088679 rufipogon NCBI temperate japonica 34 SRR1016479 rufipogon Fawcett et al. 2013 indica 35 DRR088678 rufipogon NCBI aus 36 SRR8324858 rufipogon Lou et al. 2015 indica 37 SRR8324893 rufipogon Lou et al. 2015 indica 38 SRR8324917 rufipogon Lou et al. 2015 indica 39 SRR8324921 rufipogon Lou et al. 2015 indica 40 SRR8324922 rufipogon Lou et al. 2015 indica 41 SRR8324923 rufipogon Lou et al. 2015 indica 42 ERR2245518 aus Zhao et al. 2018 indica 43 SRR1450138 nivara Ammiraju et al. 2006 indica 44 SRR1450139 nivara Ammiraju et al. 2006 indica 45 SRR1450142 nivara Ammiraju et al. 2006 aus 46 SRR1528449 nivara Ammiraju et al. 2006 aus 1References are provided at the end of the document. Table S2. List of the 358 accessions used in this study. Species Variaty Depth (X) Run accession Source1 O. sativa indica 214 ERR2242621 Zhao et al. 2018 O. sativa indica 104 ERR2245513 Zhao et al. 2018 O. sativa indica 149 ERR2245516 Zhao et al. 2018 O. sativa indica 157 ERR2245525 Zhao et al. 2018 O. sativa indica 149 ERR2242624 Zhao et al. 2018 O. sativa indica 177 ERR2245528 Zhao et al. 2018 O. sativa indica 125 ERR2245530 Zhao et al. 2018 O. sativa indica 132 ERR2245531 Zhao et al. 2018 O. sativa indica 166 ERR2245533 Zhao et al. 2018 O. sativa indica 185 ERR2242626 Zhao et al. 2018 O. sativa indica 186 ERR2245535 Zhao et al. 2018 O. sativa indica 173 ERR2245537 Zhao et al. 2018 O. sativa indica 168 ERR2245538 Zhao et al. 2018 O. sativa indica 222 ERR2245542 Zhao et al. 2018 O. sativa indica 117 ERR2245543 Zhao et al. 2018 O. sativa indica 180 ERR2241060 Zhao et al. 2018 O. sativa indica 108 ERR2245544 Zhao et al. 2018 O. sativa indica 37 ERR606786 Wang et al. 2018 O. sativa indica 50 ERR606887 Wang et al. 2018 O. sativa indica 34 ERR607071 Wang et al.
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