Domestic_v_Wild_Solanaceae_Gene_Tree_Overall

Overall gene tree generated using maximum likelihood model for FLS2 homologs from Solanaceae Domestic and Wild Species of <em>Solanum</em> (tomato, potato, eggplant), <em>Capsicum</em>, <em>Nicotiana</em>, <em>Petunia</em>, and the Solanaceae outgroup <em>Ipomoea triloba</em> (morning glory). The FLS2 coding sequences were obtained using a TBLASTN search using the FLS2 from <em>Arabidopsis thaliana</em> against Sol Genomics Database, Ensembl, and the Eggplant Genomic Database. Pseudogenes were removed and sequences were aligned using AliView. Multiple FASTA files were generated to specify by genus. Using these sequences, phylogenetic trees were generated using IQTree, a software tool that uses a maximum likelihood model. This file was utilized for the analysis used in Figure 2.

本研究构建的FLS2同源基因总基因树基于最大似然模型，所用序列来源于茄科栽培与野生物种，涉及茄属（<em>Solanum</em>，包含番茄、马铃薯、茄子）、辣椒属（<em>Capsicum</em>）、烟草属（<em>Nicotiana</em>）、矮牵牛属（<em>Petunia</em>），以及作为茄科外类群的三裂叶番薯（<em>Ipomoea triloba</em>，俗称牵牛花）。FLS2编码序列通过TBLASTN搜索获取：以拟南芥（<em>Arabidopsis thaliana</em>）的FLS2序列为查询探针，比对茄科基因组数据库（Sol Genomics Database）、Ensembl数据库及茄子基因组数据库（Eggplant Genomic Database）。随后移除假基因（Pseudogenes），并使用AliView工具完成多序列比对；按属分类生成多份FASTA格式文件（FASTA）以标注所属类群。基于上述序列，使用IQTree软件（一款基于最大似然模型的系统发育分析工具）构建系统发育树。本文件用于图2对应的分析工作。