Gene Family Analysis and Phylogenetic Analysis

Gene family clustering analysis was performed using BLASTP and OrthoMCL v2.0.9 (Li et al. 2003) based on the annotated genes of J. mimosifolia and 11 other sequenced plant species, namely, 8 Lamiales (H. impetiginosus, S. indicum, Salvia splendens, Mimulus guttatus, Striga asiatica, Utricularia gibba, Boea hygrometrica, and O. europaea), 2 Solanales (S. tuberosum and Solanumlycopersicum), and 1 rosid plants (A. thaliana). We identified 194 single-copy orthogroups across the 12 plant genomes. For each orthogroup, protein sequences were aligned using MAFFT v7.313 (Katoh et al. 2002) and conserved sites were extracted from the alignments using Gblocks v0.91b (Castresana 2000). The conserved sequences were concatenated into a single multiple sequence alignment. A maximum-likelihood phylogeny was constructed using RAxML v8.2.11 (Stamatakis 2014) under the PROTGAMMAILGX model with 100 bootstrap replicates. Then MCMCTREE in PAML v4.9e (Yang 2007) was applied to estimate the divergence time among 12 species based on the phylogenetic tree with the main parameters of burnin = 1,000,000, nsample = 20,000, and sampfreq = 150. The divergence time between A. thaliana and S. tuberosum (111–131 Ma) was obtained from the TimeTree database (http://www.timetree.org, last accessed May, 12, 2021) and used as fossil calibration point. Gene family evolution was examined across the time-calibrated phylogenetic tree using CAFÉ v3.1 (De Bie et al. 2006) with the main parameters -p = 0.05 and lambda -s.