Additional file 1: of Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Figure S1. Diagram of SNP filtering process. Figure S2. Frequency of SNP substitution types. Figure S3. Base-composition distribution for randomly sampled genic and non-genic SNPs. Figure S4. Comparison of base-composition distribution between different regions of the genome. Figure S5. Distribution of MAF for genome-wide genic and non-genic SNPs. Figure S6-S8. Base-composition distribution for genic and non-genic SNPs across chromosomes. Figure S9. Base-composition distribution at TE and non-TE regions. Figure S10. Base-composition distribution between domesticated and wild accessions and crossover rate for maize chromosomes. Figure S11-S12. Base-composition distribution between domesticated and wild accessions and recombination rate for soybean chromosomes. Figure S13-S15. Distribution of MAF calculated with genic and non-genic SNPs across chromosomes. Figure S16. Base-composition distribution at selective sweep and non-selective-sweep regions. Figure S17. Frequencies of motifs related to solar-UV signature among genic and non-genic SNPs conditional on methylated and unmethylated regions. Figure S18. Frequencies of motifs related to solar-UV signature among SNPs from pericentromeric and non-pericentromeric regions under methylated and unmethylated conditions. Figure S19. Enrichment test of mutations related to solar-UV signature with population-private SNPs. Figure S20. Distribution of f(TCG) and f(CCG) across population-private SNPs. Figure S21. Distribution of f(TCG) and f(CCG) at different genomic regions. Figure S22. GWAS-identified genomic regions underlying base-composition variation. Figure S23. GWAS tagged genes in NER pathway. Figure S24. Polymorphisms in soybean DNA ligase1. Table S1. UV-related genes are enriched near the associated loci in maize. Table S2. UV-related genes tagged by the associated SNPs in maize. Table S3. UV-related genes are enriched near the associated loci in soybean. Table S4. UV-related genes tagged by the associated SNPs in soybean. Table S5. Summary of 100 maize accessions. Table S6. Summary of 302 soybean accessions. (PDF 3092 kb)