Supplementary tables for Honey Bee symbiont buffers larvae against nutritional stress and supplements lysine

To define orthologs, protein sequences were extracted from NCBI annotated sequence files for the listed accesions (Supplementary Table 3). Reciprocal best BLAST hits were calculated, and genes clustered into ortholog groups using complete linkage. Conserved core orthologs were used to generate the species tree for these genera and this was used, in conjunction with GLOOME to infer branch-specific gene gain/loss events (Supplementary Table 2). To define presence/absence of amino acid biosynthesis genes (Supplementary Table 1), ortholog representatives were run against GapMind to find amino acid biosynthetic genes in the proteomes. Additionally, annotation based on NCBI’s PGAP was used, in conjunction with DOE’s IMG/M, to confirm the putative function of orthologous groups of genes.