Host symbiont gene reconciliation supplementary material

Biological datasets used in our Host symbiont gene phylogenetic reconciliation paper. Cinara aphids dataset was obtained from the supplementary data to Manzano-Marin et al. ISME, 2019, and we chose a representative subset of the species present in the gene trees. We used an exterior source for the phylogeny for the enterobacteria present in the gene trees using Annotree (Mendler et al., Nucleic Acids Research, 2019) (for the one that are not associated to Cinara aphids, and are thus "free living" in this setting). Helicobacter pylori dataset was constructed by Alexia Nguyen Trung, gathering available whole genome sequences on NCBI with assigned geo populations on NCBI or pubMLST.<br> A phylogenetic tree was built based on the concatenation of universal-unicopy genes (322 genes), and a sample of 113 strains representing the diversity of H. pylori in the old world (excluding strains from the Americas) was obtained using Treemmer (Menardo et al, BMC Bioinformatics, 2018).<br> Then, 6 non pylori strains were added (H. hepaticus, H. acinonychis, H. canadensis, H felis, H. bizzozeronii, H. cetorum), as an external group.<br> In this study we considered the 1034 gene families, including 322 universal unicopy family, which displayed strains from the external group and from at least 3 continents.