Fig. 4.
Phylogeny-based pangenome gene retention rates analyses and gene ontology enrichment analyses. A Reconstructed species phylogeny of barley, wild emmer, and bread wheat based on orthologous gene classification using OrthoFiner software. The numbers of hierarchical orthologous group (HOG) identified at each node were labelled. B. distachyon was included as outgroup. B Scatter plot displaying the correlation between mean GRR for each OG and gene family size (number of HOG in each OG) in barley, wild emmer, and bread wheat. C Pie chart displaying the duplication types of the identified 326 HPT2-pattern-like genes. D GO enrichment analyses of the identified HPT2-pattern-like genes displaying deceased GRR from barley to wild emmer to bread wheat. Enrichment score was calculated as −log10(p-value). E Gene network displaying the enriched biological pathways for the HPT2-pattern-like genes. Node size and color correspond to number of genes and significance level, respectively. Node edge (blue line) indicates number of overlapped gene