Fig. 1

Pangenome of Gossypium arboreum. a The gene number and presence composition of the G. arboreum pangenes. Pie charts correspond to the proportions of the core, soft core, shell, and cloud genes according to gene presence in the population. b The modeling analysis of the number of pangenes and core genes in 341 cotton accessions. The top and bottom edges represent 99% confidence intervals. c The boxplot displays the number of genes in each group. P-values (“***” indicate P <  0.01) were calculated by a two-sided Mann–Whitney U test. d Maximum-likelihood tree of the 326 known geographic accessions was constructed using the 5632 dispensable genes. e Heatmap showing the PAVs of 5632 dispensable genes in 326 accessions. K-means (K = 4) clustering was used to cluster genes. Each cluster is shown with one or two geographical distributions, and enriched GO terms in each cluster are displayed in the right panel