Extended Data Fig. 2: Phylogeny and per-genome gene content of genomes and MAGs within FGT Lactobacillus genome catalogs.
a, Phylogenetic tree of L. iners isolate genomes and MAGs as in Fig. 1b, plus isolate genomes of L. crispatus (n = 182), L. jensenii (n = 39), L. gasseri (n = 28), and L. vaginalis (n = 8). Isolates further experimentally studied in this work are indicated. The tree depicts only genome assemblies exceeding certain quality thresholds to ensure robustness of the phylogenetic reconstruction (see Methods); additional strains and genomes were included in other analyses. b, Number of genes per genome for each genome retrieved from RefSeq (“Reference Genome”), previously unreported isolate genome (“Novel Genome”), or MAG within the Lactobacillus genome catalogs analyzed in Figs. 2b and 4b and Extended Data Fig. 6a. All MAGs present in the analysis represent previously unreported assemblies (Hayward et al, manuscript in preparation, see additional information in Methods and Supplementary Tables 4-11). To maximize comprehensiveness of the pan-genomes, the catalogs included high- and medium-quality genomes and MAGs, defined as assemblies with minimum estimated completeness >50% (some of which are classified as partial assemblies by NCBI size criteria) and maximum estimated contamination <10%. Gene count analysis excludes gene sequences observed in only 1 genome or MAG per species to eliminate singleton contaminating sequences within individual genome assemblies. Box center lines, edges, and whiskers signify the median, interquartile range (IQR), minima and maxima respectively.
