Figure 3. Alignment and newick tree of new MAGs in the global lucinid symbiont tree

Concatenated alignment of 120 conserved bacterial marker genes from the MAGs was obtained with the GTDB-Tk v2.1.1 (Genome Taxonomy Database Toolkit) classify workflow, including MAGs published in this work and in Osvatic et al. 2023 ISMEJ. Maximum likelihood phylogenomic tree inferred from GTDB’s multiple sequence alignment with IQ-Tree v2.2.2.1 (Minh et al. 2020; Hoang et al. 2018; Kalyaanamoorthy et al. 2017) including MAGs published in this work and in Osvatic et al. 2023 ISMEJ. The tree was inferred with auto substitution model detection, 1,000 ultrafast bootstrap (UFB) replicates and 1,000 samples for SH-aLRT branch testing. Nodes with values of UFB greater or equal to 95% and of SH-aLRT greater or equal to 80% were considered to be strongly supported. The best-fit model was Q.plant+F+I+G4.

使用基因组分类数据库工具包（Genome Taxonomy Database Toolkit, GTDB-Tk）v2.1.1的分类流程，对来自宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）的120个保守细菌标记基因完成串联比对，所涉及的MAGs包含本研究及Osvatic等2023年发表于《ISME Journal》（ISMEJ）的序列。基于GTDB的多序列比对结果，借助IQ-Tree v2.2.2.1（Minh等人，2020；Hoang等人，2018；Kalyaanamoorthy等人，2017）构建最大似然系统发育组学树，该树涵盖的MAGs同样包含本研究及Osvatic等2023年发表于ISMEJ的序列。本次系统发育树推断采用自动替换模型检测策略，设置1000次超快速自举（UFB）重复采样与1000次SH-aLRT分支检验采样。当UFB值≥95%且SH-aLRT值≥80%时，对应系统发育节点被判定为具有强支持度。最优拟合模型为Q.plant+F+I+G4。