Fig. 2: Classification and characteristics of moso bamboo pangenome gene sets.
a The number of gene sets in the pangenome (blue) and core gene set (red) increased as a function of the number of moso bamboo accessions included in the analysis (x-axis). The error bars represent the mean values ± SDs, n = simulation times. b Compositions of the pangenome. The bar plots show the number of gene sets (y-axis) in each accession categorized by frequency (x-axis). The pie chart depicts the proportions of gene sets marked by each composition category: core, softcore, dispensable, and private gene sets. The left block shows the number of unique gene sets (bottom) and the sum of unclustered genes in each genome (hatched area). c Distribution of gene sets in different groups based on gene frequency and allele composition. The y-axis represents the four groups divided according to gene frequency across accessions, and the x-axis represents the 3 gene set groups categorized according to allele composition. All the gene sets were divided into 12 groups (core-double (19,270), core-variable (20,858), core-single (169), softcore-double (561), softcore-variable (11,772), softcore-single (330), dispensable-double (267), dispensable-variable (17,010), dispensable-single (3,702), private-double (819), private-variable (5998), and private-single (44,104)). The area of each group is proportional to the number of gene sets. d, e, and f Comparison of gene length (d), expression level (e), and tissue specificity index (Tau) (f) across the 12 gene set groups (x-axis). The y-axes show gene length in base pairs, log2(TPM + 1) expression values, and the Tau specificity index. The box plots show the medians (centerlines), interquartile ranges (boxes), and 1.5 times the interquartile ranges (whiskers). n = gene set numbers. The P-values indicating statistical significance are provided in Supplementary Tables 9–11.
