Supplementary Figure 1: The distribution of 200,481 SNPs selected for the pear array design
The SNP markers are counted in a 100-Kb window. The light-yellow color represents a low content and the navy-blue color represents a high content of SNPs (range 0–215). The red circles represent the SNP markers which are significantly associated with nine traits. The plot shows that these 200,481 SNPs selected from original 18.3 million SNPs have a uniform distribution and are appropriate to be used to further develop the pear array.
Supplementary Figure 2: Fold changes of DNA methylation levels at hyper-DMRs along nine orange chromosomes during fruit ripening
The average fold changes are calculated in a 100-Kb window. The light-orange color represents a low fold enrichment change and the dark-orange color represents a high fold enrichment change of methylation (range 0.67–0.88). The green triangles represent genes that located in regions with a fold change of DNA methylation greater than one. The plot shows that the alteration of DNA methylation at hyper-DMRs during fruit ripening is unevenly distributed across the whole orange genome, with an obvious enrichment in some specific regions, probably the centromeric heterochromatin regions.
Supplementary Figure 3: The distribution of NAC binding sites and candidate genes potentially regulated by NAC during soybean seedling development
The light- and dark-purple colors represent an enriched peak detected from the ChIP-Seq data with a low and high fold enrichment (range 2.52–14.23), respectively. Boxes and circles represent genes that are up- and down-regulated during soybean seedling development, respectively. Genes which have no significantly changes during soybean seedling development are represented by triangles. This plot shows a DNA-binding-site landscape for the NAC transcription factor and potential target genes that are probably regulated by this transcription factor during soybean seedling development.
Supplementary Figure 4: The distribution of genetic diversity within two different geographical Liriodendrongroups along 19 chromosomes
Distributions of nucleotide diversity (p) along 19 Liriodendronchromosomes among accessions came from western China (range 8.34×10-5–4.87×10-3) and eastern China (range 7.26×10-5–4.09×10-3) are plotted. The nucleotide diversity in two groups are both calculated in a 2-Mb sliding window with a 1-Mb step. The plot shows that the nucleotide diversity dynamics across the whole Liriodendrongenome within eastern and western China groups share the same pattern.