Domestic_v_Wild_Solanaceae_Gene_Tree_Individual_Genuses

Individual genus gene trees generated using the 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.

本数据集为基于最大似然模型构建的茄科（Solanaceae）栽培与野生类群FLS2同源基因的属级基因树，涉及类群包括茄属（*Solanum*，涵盖番茄、马铃薯、茄子）、辣椒属（*Capsicum*）、烟草属（*Nicotiana*）、矮牵牛属（*Petunia*），以及茄科外类群三裂叶薯（*Ipomoea triloba*，俗称牵牛花）。研究中使用的FLS2编码序列，通过以拟南芥（*Arabidopsis thaliana*）FLS2序列为探针，在Sol Genomics数据库、Ensembl数据库及茄子基因组数据库中执行TBLASTN搜索获取。序列预处理阶段剔除了假基因，并通过AliView软件完成多序列比对。按属级分类生成了多份FASTA格式的序列文件。基于上述序列，借助支持最大似然模型的系统发育分析软件IQTree构建了各属的基因树。本数据集已用于本文图2的相关分析工作。