Fig. 5
From: Genome assembly and population analysis of tetraploid marama bean reveal two distinct genome types
Evolutionary dynamics of gene families in T. esculentum and 13 related species. (A) A maximum likelihood phylogenetic tree was constructed using concatenated protein sequences from 157 single-copy orthologs of T. esculentum and 13 other species, including 12 legumes and Q. saponaria as the outgroup. Sequences were aligned using MAFFT, and the tree topology was supported by 1000 bootstrap replicates. Gene family expansion and contraction counts, calculated by CAFE, are color-coded in blue (expansion) and red (contraction). Divergence times (million years ago, Ma) are annotated on the tree nodes. (B) KEGG enrichment analysis of genes in the 1155 contracted gene families of T. esculentum. (C) KEGG enrichment analysis of genes in the 2231 expanded gene families of T. esculentum. Enriched pathways are ranked by enrichment factor. Dot size indicates the number of enriched genes, while dot color represents significance, with red denoting higher significance and purple lower significance.
