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. 2017 May 12;6:e23717. doi: 10.7554/eLife.23717

Figure 8. Footprints of an ancient endosymbiosis in the haptophyte plastid proteome.

(Panel A) indicates the number of ancestral ochrophyte HPPGs that included sequences from other algal lineages in single-gene tree analyses, and whether those algal lineages branched within or external to ochrophytes. An overview of the specific origins of proteins of ochrophyte origin in each lineage is shown in Figure 8—figure supplement 1. (Panel B) compares the number of ASAFind-derived HPPGs that are uniquely shared between hypogyristea (i) or haptophytes (ii) and one other CASH lineage. Values are given for proteins found in a majority of sub-categories in hypogyristea/ haptophytes and at least one sub-category from only one other lineage (light bars), and proteins found in a majority of sub-categories in hypogyristea/ haptophytes and a majority of sub-categories from only one other lineage (dark bars). Values that are significantly greater than would be expected through random distribution are labelled with black arrows. (Panel C) shows a schematic ochrophyte tree, with six different ancestral nodes within this tree labelled with coloured boxes, and the most probable origin point for each of the 243 haptophyte plastid-targeted proteins of probable ochrophyte origin within this tree, as inferred by inspection of the nearest ochrophyte sister-group in single-gene trees. A detailed heatmap of the ochrophyte sub-categories contained in each lineage is shown in Figure 8—figure supplement 2, and BLAST top hit analyses corresponding to each plastid-targeted protein are shown in Figure 8—figure supplement 3. (Panel D) shows the number of residues that are uniquely shared between haptophytes and each node of the ochrophyte tree for 37 genes in which there has been a clear transfer from ochrophytes to haptophytes, and entirely vertical subsequent inheritance. A similar graph, showing the earliest possible inferred origin of each uniquely shared residue, is shown in Figure 8—figure supplement 4. (Panel E) shows the number of the 12728 conserved gene families inferred to have been present in the last common haptophyte ancestor that are predicted by ASAFind to encode proteins targeted to the plastid, subdivided by probable evolutionary origin, and the number expected to be present in each category assuming a random distribution of plastid-targeted proteins across the entire dataset, independent of evolutionary origin. Evolutionary categories of proteins found to be significantly more likely (chi-squared test, p=0.05) to encode plastid-targeted proteins than would be expected by random distribution are labelled with black arrows. The evolutionary origins of the ancestral gene families are shown in Figure 8—figure supplement 5.

DOI: http://dx.doi.org/10.7554/eLife.23717.038

Figure 8.

Figure 8—figure supplement 1. Origin of proteins of ochrophyte origin in different CASH lineages.

Figure 8—figure supplement 1.

This figure profiles the evolutionary origins of proteins inferred by single-gene phylogenetic analysis to have been transferred from the ochrophytes into other lineages that have acquired plastids through secondary or more complex endosymbioses. Proteins are divided into the three major ochrophyte lineages (i.e. diatoms, chrysista, and hypogyristea); all remaining proteins (inferred to have been acquired from an ancestor of multiple ochrophyte lineages, or of ambiguous but clearly ochrophyte origin) are grouped as a final category. The haptophyte proteins that could be attributed to a specific ochrophyte lineage are particularly skewed (100/178 proteins) to origins within the hypogyristea.
DOI: http://dx.doi.org/10.7554/eLife.23717.039
Figure 8—figure supplement 2. Heatmaps of nearest sister-groups to haptophytes in ancestral ochrophyte HPPG trees.

Figure 8—figure supplement 2.

This figure shows the specific ochrophyte lineages implicated in the origin of haptophyte plastid-targeted proteins, as inferred from the nearest ochrophyte sister-groups to haptophytes in trees of 242 haptophyte proteins of probable ochrophyte origin from combined BLAST top hit and single-gene tree analysis. At the top a schematic tree diagram of the ochrophytes is shown as per Figure 1, with six major nodes in ochrophyte evolution labelled with coloured boxes. The heatmap below shows the specific distribution of sister-groups in each tree, shown as per Figure 4—figure supplement 2.
DOI: http://dx.doi.org/10.7554/eLife.23717.040
Figure 8—figure supplement 3. Internal evolutionary affinities of haptophyte plastid-targeted proteins incorporated into ancestral ochrophyte HPPGs.

Figure 8—figure supplement 3.

This figure profiles the evolutionary origins of haptophyte plastid-targeted proteins incorporated into ancestral ochrophyte HPPGs by BLAST top hit analysis. Separate values are provided for query sequences from each of the three haptophyte sub-categories (pavlovophytes, prymnesiophytes, and isochrysidales) considered within the analysis. Only sequences for which a consistent origin could be identified by both BLAST top hit and single-gene tree analysis are included. For each haptophyte lineage >50% of the sequences verified by combined analysis to be of a specific ochrophyte origin have either pelagophyte or dictyochophyte top hits.
DOI: http://dx.doi.org/10.7554/eLife.23717.041
Figure 8—figure supplement 4. Evidence for gene transfer from pelagophytes and dictyochophytes into haptophytes.

Figure 8—figure supplement 4.

(Panel A) shows the next deepest sister groups identified for haptophyte proteins of hypogyristean origin in single-gene trees. The pie chart (i) compares the number of single-gene trees in which the combined clade of haptophyte and hypogyristean proteins resolves within a larger clade comprising the ochrophyte HPPG, compared to the number that resolves in external positions, either with other lineages or as a sister-group to all other sequences within the HPPG clade. Sequences for which no clear next deepest sister group affinity could be identified are listed as ‘not determined’. The heatmap (ii) shows the specific sister-group sequences associated with 65 HPPGs in which the haptophyte sequences specifically resolve with the pelagophyte/dictyochophyte clade and for which a clear internal or external position for the haptophyte/ hypogyristean group relative to the remaining ochrophyte HPPG clade could be identified. Both analyses indicate a clear bias for haptophyte sequences branching within a deeper ochrophyte clade, not just restricted to the immediate sister-groups. (Panel B) tabulates the BLAST next best hits for haptophyte sequences for which a phylogenetically consistent (>3 consecutive top hits) top hit to hypogyristea could be identified, and pelagophyte/dictyochophyte sequences for which a phylogenetically consistent top hit to haptophytes could be identified. In each case either the largest number of sequences, or (in the case of pavlovophytes) the joint largest number of sequences for which a phylogenetically consistent next best hit could be identified resolved with diatoms, indicating that these sequences were probably present in the common ancestor of diatoms and hypogyristea, and subsequently transferred to the haptophytes.
DOI: http://dx.doi.org/10.7554/eLife.23717.042
Figure 8—figure supplement 5. Earliest possible origin points of uniquely conserved sites in haptophyte plastid-targeted proteins.

Figure 8—figure supplement 5.

This figure shows the total number of residues that are uniquely shared between a 37 proteins that have clearly been transferred between the ochrophytes and haptophytes, and are of subsequently entirely vertical origin, assuming the earliest possible origin point for each residue (i.e. in which gapped or missing positions were interpreted as identities). 87/128 of the uniquely shared residues inferred to originate within the ochrophytes were congruent to gene transfers between the haptophytes and pelagophyte and dictyochophyte clade; of these, slightly more than half (46) are inferred to have originated in a common ancestor of all hypogyristea and diatoms, consistent with the gene transfer having occurred from an ancestor of the pelagophytes and dictyochophytes into the haptophytes, rather than the converse.
DOI: http://dx.doi.org/10.7554/eLife.23717.043
Figure 8—figure supplement 6. Evolutionary origin of ancestral haptophyte genes.

Figure 8—figure supplement 6.

This figure shows the most likely evolutionary origin assigned by BLAST top hit analysis to the 12728 conserved gene families inferred to have been present in the last common haptophyte ancestor.
DOI: http://dx.doi.org/10.7554/eLife.23717.044