O previously published phylogenies (Leliaert et al ; Yoon et al). Green subcategories are in green text; red algal subcategories in red text; as well as 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 write-up 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 have been identified in diverse numbers green subcategories (plotted around the xaxis) and red subcategories (plotted around 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 numerous chlorophyte subcategories but towards the exclusion of streptophytes; and to individual chlorophyte subcategories only. A detailed heatmap with the evolutionary distribution in the green subcategories detected in every single sistergroup is shown in Figure figure supplement , as well as the distribution of BLAST top rated hits inside 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 happen to be subsequently completely Lithospermic acid B web vertically inherited in all big photosynthetic eukaryotic lineages, to become uniquely TMS shared between ochrophytes and some but not all green lineages, hence could possibly represent precise synapomorphic residues. Residues are categorized by inferred origin point inside the tree topology shown in panel A, i.e each and every of the five ancestral nodes labelled. A final category shows all of the residues inferred to become particularly shared with a single green subcategory, and not with any other. The distribution of residues depending on the earliest attainable origin point (taking into account gapped and missing residues in every HPPG alignment) is shown in Figure figure supplement . (Panel E) shows the number of the conserved gene households inferred to possess been present within the last prevalent ochrophyte ancestor which can be predicted by ASAFind to encode proteins targeted towards the plastid, subdivided by probable evolutionary origin, as well as the quantity expected to be present in each category assuming a random distribution of plastidtargeted proteins across the complete dataset, independent of evolutionary origin. Evolutionary categories of proteins discovered to become substantially a lot more probably (chisquared test, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17319469 p.) to encode plastidtargeted proteins than will be anticipated 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 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 . 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 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 inside the green algal tree inspected in subsequent analyses are labelled with Figure continued on subsequent pageDorrell et al. eLife ;:e. DOI.eLife. ofResearch short article 
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 unique 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 (like chlorophytes and streptophytes); to various chlorophyte subcategories but for the exclusion of streptophytes; and to individual chlorophyte subcategories only. A detailed heatmap with the evolutionary distribution in the green subcategories detected in each sistergroup is shown in Figure figure supplement , and the distribution of BLAST top rated hits within every single subcategory is shown in Figure figure supplement . (Panel D) lists the amount of residues inferred from a dataset of ochrophyte HPPGs of verified green origin, which have been subsequently entirely vertically inherited in all important photosynthetic eukaryotic lineages, to become uniquely shared amongst ochrophytes and some but not all green lineages, therefore may well represent distinct synapomorphic residues. Residues are categorized by inferred origin point inside the tree topology shown in panel A, i.e each and every of your 5 ancestral nodes labelled. A final category shows all the residues inferred to be especially shared with one particular green subcategory, and not with any other. The distribution of residues determined by 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 households inferred to have been present within the last prevalent ochrophyte ancestor which might be predicted by ASAFind to encode proteins targeted to the plastid, subdivided by probable evolutionary origin, as well as the number anticipated to become present in each and every category assuming a random distribution of plastidtargeted proteins across the entire dataset, independent of evolutionary origin. Evolutionary categories of proteins identified to become considerably additional most likely (chisquared test, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/17319469 p.) to encode plastidtargeted proteins than could be expected 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 accessible 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 . Particular 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.