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.

本研究下载了曼陀罗（Datura stramonium，简称D. stramonium）的全基因组，以提取萜烯合酶（Terpene Synthases，TPSs）基因，并采用AUGUSTUS基因预测软件（Stanke等，2006）完成基因预测。所有序列均已上传，并以茄科（Solanaceae）物种作为参考基因组完成序列比对与定位。最终共获得366000个基因，并通过CDHIT工具（Qingyu Chen等，2016）去除基因冗余。将筛选得到的TPSs基因以1E-5为阈值，分别与NCBI、UNIPROT数据库及11个茄科物种的基因组进行基础局部比对搜索工具（Basic Local Alignment Search Tool，BLAST）比对。从绿色植物界（Viridiplantae）下载所有TPSs序列，随后进行蛋白质序列比对；保留相似度≥80%且覆盖度≥70%的比对命中结果用于后续分析。采用T-coffee（Wallace等，2006）、MUSCLE v3.8（Edgar，2004）及MAFF v6完成蛋白质序列的多序列比对。