Marker gene alignment for phylogenetic symbiont tree

All available MAGs (irrespective of completion) were used to generate a concatenated gene tree. The CheckM version 1.1.3 lineage workflow was used to locate, align, and concatenate the default set of 43 universal marker genes. Checkm’s automatically generated concatenated protein alignment of these 43 marker genes was then submitted to the W-IQ-TREE server using the default settings (auto substitution model detection, 1000 ultrafast bootstraps, and 1000 replicates of SH-aLRT branch tests).所有可用的宏基因组组装基因组（Metagenome-Assembled Genomes，MAGs），无论其组装完整度如何，均被用于构建串联基因树。本研究使用CheckM版本1.1.3的谱系分析流程，对默认的43个通用标记基因集进行定位、比对并串联。随后将CheckM自动生成的该43个标记基因的串联蛋白比对文件，以默认参数提交至W-IQ-TREE服务器，默认参数包括自动替换模型检测、1000次超快速自举检验以及1000次SH-aLRT分支检验重复。