gyrB phylogeny of 40 Agrobacterium spp.

We searched the gyrB gene sequences in 40 Agrobacterium spp. genomes using BLASTN, extracted them using a custom Python script and then aligned with ClustalOmega.A ML phylogeny was then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.本研究利用BLASTN（核苷酸局部比对工具）在40个农杆菌属（Agrobacterium spp.）物种的基因组中检索促旋酶B亚基基因（gyrB gene）序列，通过自定义Python脚本提取该基因序列，并使用ClustalOmega完成多序列比对。随后，基于上述比对结果，借助RAxML-NG 1.0.0构建最大似然（ML）系统发育树，采用参数"--model GTR+G4 --all"；该参数指定使用GTR+FO+G4m模型，同时执行20次独立推演：其中10次以随机生成的系统发育树为初始树，另外10次以经简约法优化的系统发育树为初始树，最终保留20次推演中得到的最优最大似然树。分支节点的支持度通过200棵费尔森斯坦自举树（Felsentein bootstrap trees）进行估算。