Figure 3B. Placement of new MAGs in the global lucinid symbiont tree reveals patchiness in the distribution of nitrogen fixation genes, even within species clades - Alignment and newick 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.

从本研究及Osvatic等2023年发表于《ISME Journal》（ISMEJ）的宏基因组组装基因组（Metagenome-Assembled Genomes，MAGs）中提取的120个保守细菌标记基因的串联比对结果，通过GTDB-Tk v2.1.1（基因组分类数据库工具包，Genome Taxonomy Database Toolkit）的分类工作流获取。基于GTDB的多序列比对结果，使用IQ-Tree v2.2.2.1（Minh等，2020；Hoang等，2018；Kalyaanamoorthy等，2017）构建最大似然系统发育组学树，所用样本涵盖本研究及Osvatic等2023年发表于《ISME Journal》（ISMEJ）的宏基因组组装基因组（MAGs）。该树的构建采用自动替换模型检测策略，设置1000次超快速自举（UFB）重复抽样与1000次SH-aLRT分支检验抽样。当UFB值≥95%且SH-aLRT值≥80%时，对应节点被判定为具有强支持度。最优拟合模型为Q.plant+F+I+G4。