O previously published phylogenies (Leliaert et al ; Yoon et al). Green subcategories are in green text; red algal subcategories in red text; and also other subcategories are in blue text. Five ancestral positions within the green algal tree inspected in subsequent analyses are labelled with order JNJ-42165279 Figure continued on subsequent pageDorrell et al. eLife ;:e. DOI.eLife. ofResearch report Figure continuedCell Biology Genomics and Evolutionary Biologycoloured boxes. (Panel B) shows the amount of HPPGs of verified red (red bars) or green origin (green bars) for which orthologues were identified in various numbers green subcategories (plotted around the xaxis) and red subcategories (plotted around the zaxis). An equivalent graph showing only HPPGs for which a glaucophyte orthologue was detected is shown in Figure figure supplement . (Panel C) compares the amount of trees in which HPPGs of verified green origin resolve as a sister group to all green lineages (like chlorophytes and streptophytes); to multiple chlorophyte subcategories but for the exclusion of streptophytes; and to individual 
chlorophyte subcategories only. A detailed heatmap on the evolutionary distribution on the green subcategories detected in each and every sistergroup is shown in Figure figure supplement , along with the distribution of BLAST leading hits within every subcategory is shown in Figure figure supplement . (Panel D) lists the number of residues inferred from a dataset of ochrophyte HPPGs of verified green origin, which have been subsequently entirely vertically inherited in all key photosynthetic eukaryotic lineages, to become uniquely shared amongst ochrophytes and a few but not all green lineages, hence may represent specific synapomorphic residues. Residues are categorized by inferred origin point inside the tree topology shown in panel A, i.e each and every on the 5 ancestral nodes labelled. A final category shows all of the residues inferred to become especially shared with one particular green subcategory, and not with any other. The distribution of residues according to the earliest doable origin point (taking into account gapped and missing residues in each HPPG alignment) is shown in Figure figure supplement . (Panel E) shows the number of the conserved gene households inferred to possess been present in the final common ochrophyte ancestor which might be predicted by ASAFind to encode proteins targeted to the plastid, subdivided by probable evolutionary origin, as well as the quantity expected to become present in each and every category assuming a random distribution of plastidtargeted proteins across the complete dataset, independent of evolutionary origin. Evolutionary categories of proteins identified to be substantially extra likely (chisquared test, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17319469 p.) to encode plastidtargeted proteins than will be expected are labelled with black arrows. An equivalent distribution of plastidtargeted proteins inferred employing HECTAR is shown in Figure figure supplement . DOI.eLife The following figure supplements are readily available for figure Figure supplement . Sampling richness linked with ancestral HPPGs of green algal origin. DOI.eLife Figure supplement . Heatmaps of nearest sistergroups of ancestral HPPGs of verified green origin. DOI.eLife Figure supplement . Precise origins of green HPPGs as inferred from BLAST top hit analyses. DOI.eLife Figure supplement . Earliest evolutionary 
origins of shared plastid residues. DOI.eLife Figure supplement . Origins and HECTAR primarily based targeting tests of proteins encoded by conserved ochrophyte gene clusters. DOI.eLifefigure.O previously published phylogenies (Leliaert et al ; Yoon et al). Green subcategories are in green text; red algal subcategories in red text; along with other subcategories are in blue text. 5 ancestral positions within the green algal tree inspected in subsequent analyses are labelled with Figure continued on subsequent pageDorrell et al. eLife ;:e. DOI.eLife. ofResearch report Figure continuedCell Biology Genomics and Evolutionary Biologycoloured boxes. (Panel B) shows the amount of HPPGs of verified red (red bars) or green origin (green bars) for which orthologues had been identified in different numbers green subcategories (plotted on the xaxis) and red subcategories (plotted on the zaxis). An equivalent graph displaying only HPPGs for which a glaucophyte orthologue was detected is shown in Figure figure supplement . (Panel C) compares the number of trees in which HPPGs of verified green origin resolve as a sister group to all green lineages (like chlorophytes and streptophytes); to several chlorophyte subcategories but for the exclusion of streptophytes; and to individual chlorophyte subcategories only. A detailed heatmap with the evolutionary distribution with the green subcategories detected in each and every sistergroup is shown in Figure figure supplement , plus the distribution of BLAST major hits within each subcategory is shown in Figure figure supplement . (Panel D) lists the number of residues inferred from a dataset of ochrophyte HPPGs of verified green origin, which happen to be subsequently entirely vertically inherited in all key photosynthetic eukaryotic lineages, to become uniquely shared involving ochrophytes and some but not all green lineages, hence may well represent precise synapomorphic residues. Residues are categorized by inferred origin point inside the tree topology shown in panel A, i.e each in the five ancestral nodes labelled. A final category shows all of the residues inferred to become especially shared with a single green subcategory, and not with any other. The distribution of residues based on the earliest possible origin point (taking into account gapped and missing residues in each HPPG alignment) is shown in Figure figure supplement . (Panel E) shows the amount of the conserved gene families inferred to possess been present inside the final frequent ochrophyte ancestor that happen to be predicted by ASAFind to encode proteins targeted Nigericin (sodium salt) towards the plastid, subdivided by probable evolutionary origin, plus the number expected to become present in every category assuming a random distribution of plastidtargeted proteins across the complete dataset, independent of evolutionary origin. Evolutionary categories of proteins identified to be significantly extra likely (chisquared test, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17319469 p.) to encode plastidtargeted proteins than would be anticipated are labelled with black arrows. An equivalent distribution of plastidtargeted proteins inferred utilizing HECTAR is shown in Figure figure supplement . DOI.eLife The following figure supplements are obtainable for figure Figure supplement . Sampling richness associated with ancestral HPPGs of green algal origin. DOI.eLife Figure supplement . Heatmaps of nearest sistergroups of ancestral HPPGs of verified green origin. DOI.eLife Figure supplement . Specific origins of green HPPGs as inferred from BLAST major hit analyses. DOI.eLife Figure supplement . Earliest evolutionary origins of shared plastid residues. DOI.eLife Figure supplement . Origins and HECTAR primarily based targeting tests of proteins encoded by conserved ochrophyte gene clusters. DOI.eLifefigure.