Fig. 2

Clustering of secreted and non-secreted plant proteins into orthogroups reveals species-specific and genus-specific gene families for shoot and root parasitic plants. a A STAG (Species Tree inference from All Genes) species tree inferred from single-copy orthogroups (OGs). The STAG support values at internal nodes denote the proportion of times that the bipartition was observed for each species tree estimated from each OG. Scale denotes the average number of amino acid substitutions per site. Sh: Striga hermonthica, Sa: Striga asiatica, Mg: Mimulus guttatus, Ca: Cuscuta australis, Cc: Cuscuta campestris, In: Ipomoea nil, At: Arabidopsis thaliana. The table shows the number of OGs specific to either the species, or genus, or at the level that includes the non-parasitic outgroup. OG counts are divided into three groups: consisting entirely of non-secreted proteins (non-secreted), entirely of secreted proteins (secreted) or a mix of non-secreted and secreted proteins (mixed). b The proportion of secreted or mixed OGs at the genus and non-parasitic outgroup level. Counts are given at the base of each bar. c An ultrametric tree for the plant species used in this study showing the numbers of significantly expanded OGs for each branch. The numbers in bold denote the number of expanded OGs for each branch. For a and c, the numbers in parenthesis represent the numbers of non-secreted or secreted proteins found in all the OG at each level. Numbers highlighted red or green represent the putative secreted proteins found in OGs that were either specific to (a) or expanded in (c) the Striga or Cuscuta genera, respectively