Fig. 1

Phylogenetic distribution of 54,085 genomes across 183 species selected for core genome analysis. a Phylogenetic tree of species’ representatives with respect to class, with branch lengths derived from the Web of Life tree. Representatives were based on the most recent common ancestors of selected species’ genomes in the original tree. b Pangenome construction workflow applied to each species to encode species-wide gene-level variation as binary matrices. c Statistical model for estimating each genome’s gene recovery rate (fraction of genes recovered in the final genome assembly) and each gene’s true frequency from species’ pangenome matrices