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Additional file 2: Table S1. The results of 80 cultivated and wild rice genomes survey. Table S2. Summary of Nanopore Technologies sequencing data of JX1 and SL1 genome. Table S3. Summary of sequencing assembly data of JX1 and SL1 genome. Table S4. Details of the 12 pseudo-chromosomes of JX1 and SL1. Table S5. Summary of sequencing evaluation data of JX1 and SL1genome. Table S6. Repetitive elements in JX1 and SL1 genomes. Table S7. The information of full length transcriptome sequencing data of JX1 and SL1. Table S8. The transcriptome sequencing data from different tissues of JX1 and SL1 based on Illumina sequence. Table S9. Annotated predictions of gene structure. Table S10. Summary of the assembly of 13 cultivated and wild rice genomes. Table S11. The SV information for 13 cultivated and wild rice. Table S12. Sequence information for structural variation. Table S13. The annotation of SV. Table S14. The sample list for SV population analysis. Table S15. The significant association sites based on GWAS data. Table S16. 49 cloned genes overlapping with DELs (>10 kb) region.

Additional file 1: Fig. S1. (a) Geographic origins of cultivated and wild rice accessions in this study. (b) SNP-based phylogenetic tree based on short-read sequencing of more than 600 cultivated and wild rice accessions. Major taxonomic groups are marked by colored lines along the circumference. Colored dots indicate a subset of the 80 accessions selected for genome survey. Fig. S2. Chromosome karyotyping of JX1 (a) and SL1 (b) in meiosis period in the root tip. Fig. S3. Distribution of short reads mapped on corresponding genome assemblies. (a) is JX1 and (b) is SL1. Fig. S4. Dot plots of assembly comparisons between JX1 and Nipponbare (a) and between SL1 and Nipponbare (b). Fig. S5. Relationship between SVs and their surrounding genes. Fig. S6. Venn-like diagram presenting the numbers of SVs among indica, japonica, and wild rice. Fig. S7. For each SV, the distance to the telomeric (a) and centromeric regions (b) of each chromosome was calculated and divided into 100-kb bins. (c) SV densities of short/long chromosome arms in continuous 200-kb windows. Significance was tested by Fisher’s exact test; NA indicates p > 0.05. Fig. S8. PCA plots of cultivated and wild rice accessions based on SV diversities. The three subgroups are indicated in different colors at the top of the Fig. Fig. S9. Phenotypes of the rice population used for GWAS, include FLL (flag leaf length), FLW (flag leaf width), GL (grain length), GW (grain width), PB (primary branch), PH (plant height), SB (secondary branch), and TGW (1000 grain weight). Fig. S10. GWASs on FLL, FLW, GL, GW, PB, PH, SB, and TGW using the compressed MLM. Manhattan plots for these phenotypes. The log10-transformed P values from a genome-wide scan were plotted against the position on each of the 12 chromosomes. Quantile-quantile plot for these phenotypes. The horizontal axis shows log10-transformed expected P values, and the vertical axis indicates log10-transformed observed P values. Fig. S11. (a) XP-CLR scores calculated by SNPs comparing wild rice with cultivated rice. (b) XP-CLR scores calculated by SVs comparing wild rice with cultivated rice. Chromosomes are painted with either blue or orange and the black line is defined using the top 5% XP-CLR scores.