Fig. 3

Comparative genomics analysis between P. giganteum and P. purpureum. a Histogram showing the distribution of protein sequence similarity between P. giganteum and P. purpureum. x-axis represents the intervals of percent similarity, and y-axis represents the number of homologous gene pairs. The inset pie chart represents the number and percentage of P. giganteum genes having significant BLAST hits against P. purpureum genes. b Venn diagram showing the common and unique orthogroups (OGs) identified in subgenomes of P. giganteum and P. purpureum. In total, 31,314 OGs were assigned by OrthoFinder, of which 11,888 were commonly detected in four subgenomes. c Genome-wide synteny analysis between P. giganteum and P. purpureum using JCVI. A total of 24,107 syntenic gene pairs were obtained through inter-genomic comparison. Nearly all the chromosomes exhibited 1:1 correspondence between two Pennisetum species. However, many genome rearrangements were observed between two species. d Statistics of structural variations (SVs) identified between P. giganteum and P. purpureum through SyRI analysis. SVs are categorized into four major types, including deletion, insertion, inversion, and translocation. The upper panel denotes the number of four types of SVs in the A and B subgenomes, and the lower panel represents the cumulative length of four types of SVs in two subgenomes. The A subgenome is shaded in green, and the B subgenome is highlighted in orange. The cumulative length of different types of SVs was calculated with the P. giganteum as the reference. e Visualization of genome structural rearrangements using the visualization tool plotsr. The left panel denotes the result of the A subgenome, and the right panel represents the result of the B subgenome. Each graph was composed of a pair of homologous chromosomes. The color of the links denotes the type of annotations: (1) syntenic regions are shaded in gray; (2) inversions are highlighted in orange; (3) translocations are colored in green; and (4) duplications are shaded in blue. f Box and whisker plot showing the distribution of nonsynonymous to synonymous substitution ratios (Ka/Ks) in two subgenomes of P. giganteum and P. purpureum. The upper and lower vertical extending lines denote the most extreme values within 1.5 interquartile range of the 75th and 25th percentile of each group, respectively. The dots above the upper line denote the outliers. The number of gene pairs used for Ka/Ks calculation was listed below the boxplot for each subgenome. Statistical significance was determined using two-sided Wilcoxon rank-sum test