Fig. 2

The features of the gene and orthologous group PAVs. A Distributions of the core and dispensable genes along with features, including gene age, gene length, number of genes per orthologous group, maximum expression, number of expressed tissues, pan-Zea Tajima’s D value, and dN/dS between the teosinte and maize populations. The gray histograms in C–H are the distributions of counts for each feature item. B, C Distributions of the PAV matrices for the dispensable genes (B) and the orthologous groups (C) according to the clusters and populations. X- and Y-axes represent the individuals and genes (or orthologous groups), with the top-most and right-most bars indicating the cluster information and sub-population groups, respectively. D The lollipop plots of the GO enrichment analyses (GOEA) and KO enrichment analyses (KOEA) of each gene cluster, with the X- and Y-axes indicating the fold enrichment and each enriched item, respectively. The point size indicates the P-value (only records with corrected Q values < 0.05 were plotted). E The heatmap plot indicates the KEGG pathways enriched in maize and concentrated in the orthologous group clusters (oCLS10–13) when compared to the pan-Zea scatted clusters (oCLS1–5). The color gradient indicates the number of KOs related to the current pathway. F Sankey plot of the proportions of unbalanced sub-group genes. G, H The distributions of random (G) and unbalanced (H) genes along the domestication (DOM) and adaptation (ADAPT) selective sweep regions. Background, regions that were not in the top 5% of the selective sweep signals. I Features of maize-specific and teosinte-specific genes. Shared legends with A, F, and G. The Z-scores and P-values were calculated from 10,000 permutations of the Wilcoxon-Mann-Whitney test. TEO, teosinte; TST, tropical/subtropical maize; TEM, temperate maize; RANDOM, balanced across groups; NA, not available due to core or lost in the entire group; the enriched genes were further divided into two categories: “Fixed”, present in all individuals of the current group, and “Specific”, present specifically in the current group (absent in all individuals of the other groups)