TPS gene analysis

We downloaded the whole genome of D. stramonium to extract the TPSs genes and gene prediction was performed using AUGUSTUS (Stanke et al., 2006). All sequences que uploaded and mapped using as reference species of Solanaceae. A total of 366 000 genes were extracted, and gene redundancy was reduced with CDHIT (Qingyu Chen et al., 2016). The selected TPSs genes were blasted against the NCBI, UNIPROT databases, and the 11 genomes of Solanaceae, using a threshold value of 1E-5. All TPSs were downloaded from Viridiplantae followed by a protein-protein blast; hits above 80% of similarity and 70% of cover were saved for further analyses. Meta-alignments of protein sequences were performed using T-coffee (Wallace et al. 2006), MUSCLE v3.8 (Edgar 2004) and MAFF v6.