Fig. 3

Species and gene phylogenetic trees for the carrot, coffee and grape genomes. a Phylogenetic tree of carrot (D), coffee (C), and grape (V): ECH is denoted by blue lightning bolts, and the two carrot paleotetraploidization events are denoted by red lightning bolts. b Gene phylogeny: three paralogous genes in the grape and coffee genomes are denoted by V1, V2, V3 and C1, C2, C3, produced by the ECH, and each has four orthologs and eight outparalogs in the carrot genome. For example, V1 has four orthologs D11, D12, D13, and D14 and eight outparalogs D21, D22, D23, D24, D31, D32, D33, and D34 in carrot. The species tree was produced based on our present analysis of homologous genes