Additional file 3:

Annotations for the Cardinium genome from four platforms (IMG/M, Kbase, Rast, MG-Rast) were compared with the manual annotation conducted by Santos-Garcia et al. 2014. The JGI platform had both the absolute highest number of Enzyme Commission (EC) predictions as well as the highest overlap with the manual annotation. Hence, it was selected as the standard annotation tool for all symbionts. (DOCX 113 kb

Additional file 2:

Comparison of the completeness of the draft genomes using CheckM. (XLS 32 kb

Additional file 8:

Categorization of the complementary metabolites produced in each combination of two symbionts into different metabolic pathways in the host environment with and without consideration of the metabolic contribution of Portiera aleyrodidarum. (XLS 55 kb

Additional file 9:

Orthologous protein clusters of five Wolbachia strains represented as a Euler–Venn Diagram, as described in additional file 1. (DOCX 187 kb

Additional file 11:

Illustration of the putative complementation at metabolic level detected for the synthesis of Branched Chain Amino Acids and Lysine. The Wolbachia’s lysine biosynthetic pathway lacks its last reaction (argD, EC 4.1.1.20), which is present in Hamiltonella, leading to a complementary potential production of lysine from M-DAP. Synthesis of M-DAP is consistently inferred in most sequenced Wolbachia, providing an intermediate compound for the biosynthesis of peptidoglycan, part of the bacterial membrane. (DOC 108 kb

Additional file 10:

Comparison of annotations retrieved for the four different Porteria genomes using the JGI platform. (DOCX 111 kb

Additional file 12:

Co-occurrence frequencies of facultative endosymbionts. (DOC 86 kb

Additional file 7:

Illustration of the model used to simulate growth, calculate metabolic overlap, and estimate the effect of specific metabolites on metabolic production. (DOCX 179 kb

Additional file 1:

Description of symbiont’s DNA extraction and Wolbachia genome assembly. (DOCX 26 kb

Additional file 4:

List of the Enzyme Commission (EC) numbers for endosymbionts used in the analyses. (XLS 79 kb