FIG. S1. Genome alignment of rufipogon, indica and japonica against O. longistaminata performed using MUMmer. A large inversion, marked using a blue circle, was found in indica accessions. 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 1D 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 (Pearson r) between genetic diversity (π) of SVs and that of SNPs and indels in rufipogon (A), indica (B), and japonica (C). FIG. S8. The additive, heterozygous and recessive (homozygous) burden for three taxa and various categories of SV. See figure 3A of the main text to see the additive, heterozygous and recessive burden for all of SV. FIG. S9. 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. S10. 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. S11. 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. S12. 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. S13. 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 supplementary figure S12, Supplementary Material online. FIG. S14. Graphs (A), (B) and (C) illustrate the SFS calculated by PoPoolationTE2 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. FIG. S15. The SFS of TE families in rufipogon (A), indica (B), japonica (C) were detected by TE-locate. Table S1. The number of variants detected by Illumina short reads, PacBio long reads, and genome alignment. Genome alignment Variant type Illumina PacBio LASTZ MUMmer rufipogon Number of sample 90 1 1 TRA 73,051 182 DUP 21,090 1,121 0 DEL 52,946 22,367 12,978 INV 178,141 37 73 INS 27,460 24 MEI 280,556 44,832 123,896 indica Number of sample 96 6 6 6 TRA 49,144 76,146 1,143 DUP 45,404 197 1,646 1 DEL 27,188 58,621 33,551 12,788 INV 261,158 11,081 105 227 INS 88,336 28,284 66 MEI 280,904 269,104 66,599 221,790 japonica Number of sample 106 3 6 6 TRA 40,370 9,797 221 DUP 3,905 8 1,797 1 DEL 21,325 7,134 28,773 25,919 INV 259,990 807 67 74 INS 23,610 35,308 49 MEI 246,979 52,572 89,723 49,494 All taxa Number of sample 347 10 14 TRA 76,835 85,279 1,332 DUP 48,132 213 3,700 2 DEL 72,930 60,747 62,953 48,153 INV 341,752 11,532 159 343 INS 103,447 70,065 113 MEI 284,741 270,708 246,340 Table S2. The details of assembled genomes used in this study. Infraspecific name Sequencing Species NCBI BioProject Assembly level Reference (Abbr.) technology indica Zhenshan 97 (ZS97) PRJNA302542 PacBio ~120X Chromosome Zhang et al. 2016a Shuhui 498 (R498) PRJNA318714 PacBio ~120X Chromosome Du et al. 2017 Minghui 63 (MH63) PRJNA302543 Pacbio ~120X Chromosome Zhang et al. 2016a IR8 PRJNA353946 PacBio ~70X Chromosome Stein et al. 2018 93-11 PRJNA427873 PacBio ~116X Chromosome Zhang et al. 2018 https://www.ncbi.nlm.nih.gov/as Tetep PRJNA482013 PacBio ~148X Chromosome sembly/GCA_004348155.2 japonica HEG4 PRJNA264749 Illumina ~220X Chromosome Lu et al. 2017 Nipponbare (IRGSP) PRJDB1747 Illumina Chromosome IRGSP 2005 Nipponbare (Nippo) PRJNA427870 PacBio ~117X Chromosome Zhang et al. 2018 https://www.ncbi.nlm.nih.gov/as Hitomebore (Hitom) PRJDA67163 Illumina ~179X Chromosome sembly/GCA_000321445.1 Suijing18 PRJNA396093 PacBio ~62X Contig Nie et al. 2017 KitaakeX PRJNA234782 PacBio ~100X Scaffold Jain et al. 2019 rufipogon W1943 PRJEB4137 Illumina ~130X Scaffold Stein et al. 2018 O. longistaminata PRJDB6339 PacBio ~66X Chromosome Reuscher et al. 2018 Table S3. Functional annotation of significantly divergent (top 1% FST) genes between each pairst of taxa (rufipogon, indica and japonica). Gene ID (MSU7) Gene ID (IRGSP1.