Individual marker gene and MLSA phylogenies

CDS alignments and gene trees were extracted from the ‘41NeoPseudo’ Pantagruel database (Dataset https://doi.org/10.6084/m9.figshare.8320142) for the following genes atpD (gene family id: RHIZOC034665, OG id: 1), glnII (RHIZOC002590, 0), gyrB (RHIZOC002739, 0), recA (RHIZOC040013, 0) and rpoB (RHIZOC004093, 0). Note that R. marinum MGL06^T sequence for glnII gene was missing in gene family RHIZOC002590, probably due to incomplete genome assembly. CDS alignments were concatenated and a tree was computed with MrBayes as described in Dataset https://doi.org/10.6084/m9.figshare.8320199.

编码序列（Coding Sequence, CDS）比对与基因树均从“41NeoPseudo” Pantagruel数据库（数据集链接：https://doi.org/10.6084/m9.figshare.8320142）中提取，涵盖以下基因：atpD（基因家族ID：RHIZOC034665，同源基因家族（Orthologous Group, OG）ID：1）、glnII（RHIZOC002590，OG ID：0）、gyrB（RHIZOC002739，OG ID：0）、recA（RHIZOC040013，OG ID：0）及rpoB（RHIZOC004093，OG ID：0）。需注意，基因家族RHIZOC002590中缺少海生根瘤菌（Rhizobium marinum）MGL06^T的glnII基因序列，该缺失大概率由其基因组组装不完整所致。随后将所有CDS比对结果进行拼接，并使用MrBayes软件构建系统发育树，具体流程参照数据集https://doi.org/10.6084/m9.figshare.8320199中的描述。