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 inside the green algal tree inspected in subsequent analyses are labelled with Figure continued on subsequent pageDorrell et al. eLife ;:e. DOI.eLife. ofResearch write-up Figure continuedCell Biology Genomics and Evolutionary Biologycoloured boxes. (Panel B) shows the number of HPPGs of verified red (red bars) or green origin (green bars) for which orthologues have been identified in various numbers green subcategories (plotted on 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 (such as chlorophytes and streptophytes); to a number of chlorophyte subcategories but to the exclusion of streptophytes; and to person chlorophyte subcategories only. A detailed heatmap with the evolutionary distribution on the green subcategories detected in every single sistergroup is shown in Figure figure supplement , plus the distribution of BLAST best hits inside 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 in between ochrophytes and some but not all green lineages, hence could represent certain synapomorphic residues. Residues are categorized by inferred origin point within the tree topology shown in panel A, i.e each with the five ancestral nodes labelled. A final category shows all of the residues inferred to be specifically shared with one particular 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 number of the conserved gene households inferred to possess been present inside the last widespread ochrophyte ancestor which might be predicted by ASAFind to encode proteins targeted for the plastid, subdivided by probable evolutionary origin, and the number anticipated to be present in each and every category assuming a random distribution of plastidtargeted proteins across the whole dataset, independent of evolutionary origin. Evolutionary categories of proteins found to become drastically much more probably (MP-A08 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 using HECTAR is shown in Figure figure supplement . DOI.eLife The following figure supplements are out there 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 . Certain origins 
of green HPPGs as inferred from BLAST prime hit analyses. DOI.eLife Figure supplement . Earliest evolutionary origins of shared order McMMAF plastid residues. DOI.eLife Figure supplement . Origins and HECTAR 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; and also other subcategories are in blue text. 5 ancestral positions within the green algal tree inspected in subsequent analyses are labelled with Figure continued on next pageDorrell et al. eLife ;:e. DOI.eLife. ofResearch article Figure continuedCell Biology Genomics and Evolutionary Biologycoloured boxes. (Panel B) shows the number of HPPGs of verified red (red bars) or green origin (green bars) for which orthologues were identified in distinctive numbers green subcategories (plotted around the xaxis) and red subcategories (plotted on 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 numerous chlorophyte subcategories but to the exclusion of streptophytes; and to individual chlorophyte subcategories only. A detailed heatmap of your evolutionary distribution in the green subcategories detected in each sistergroup is shown in Figure figure supplement , as well as the distribution of BLAST prime hits within every single 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 significant photosynthetic eukaryotic lineages, to be uniquely shared between ochrophytes and some but not all green lineages, therefore could possibly represent certain synapomorphic residues. Residues are categorized by inferred origin point inside the tree topology shown in panel A, i.e every single in the 5 ancestral nodes labelled. A final category shows all of the residues inferred to become specifically shared with 1 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 every single HPPG alignment) is shown in Figure figure supplement . (Panel E) shows the number of the conserved gene families inferred to possess been present within the final prevalent ochrophyte ancestor which might be predicted by ASAFind to encode proteins targeted for the plastid, subdivided by probable evolutionary origin, and also the number anticipated to become present in every single category assuming a random distribution of plastidtargeted proteins across the entire dataset, independent of evolutionary origin. Evolutionary categories of proteins located to become drastically a lot more most 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 applying HECTAR is shown in Figure figure supplement . DOI.eLife The following figure supplements are obtainable for figure Figure supplement . Sampling richness related 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 . Certain origins of green HPPGs as inferred from BLAST best hit analyses. DOI.eLife Figure supplement . Earliest evolutionary origins of shared plastid residues. DOI.eLife Figure supplement . Origins and HECTAR based targeting tests of proteins encoded by conserved ochrophyte gene clusters. DOI.eLifefigure.