Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

Abstract

Background: How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, and two aplastidic sister taxa, Phytophthora ramorum and P. sojae.

Results: Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes.

Conclusion: Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different a priori assumptions inherent in competing evolutionary hypotheses.

Figure 1

Specific tests of the chromalveolate versus ochrophyte-specific models. A. The chromalveolate model assumes the plastid present in modern ochrophytes was adopted as a red algal endosymbiont in the distant ancestor of all chromalveolate taxa, meaning this plastid was lost from oomycetes after they diverged from ochrophytes. Thus, the model (H₁: yellow box and arrows) makes explicit and testable predictions. In contrast, an ochrophyte-specific origin of the diatom plastid (H₂: orange box and arrow) makes alternative predictions. B. Fisher exact tests for excess gene signal in heterokont genomes from red algae versus the amoebozoan control. When adjusted for genome size, there are proportionally more first hits to red algae than to amoebozoans in P. ramorum but not in P. sojae. Both diatom genomes display highly significant excess signal from red algal genes. C. The same tests on only those genes present in all eukaryotic groups, showing the strong red signal in diatoms is not simply from plastid-related genes. D. Same tests (on genes present in all eukaryotic groups) on second hits when the first hit is to the sister heterokont. There is no indication of an excess red algal signal in either oomycete genome. More significantly, the extraordinary signal for a red contribution to the diatom genomes disappears in gene specifically conserved between oomycetes and diatoms. Significant results after adjustments for multiple tests in B-D are shown in blue bold text.

Figure 2

Regressions showing red algal signal in diatoms is not shared with oomycetes. A. Regressions on second hits for genes that are present in all eukaryotic groups (therefore, unrelated to plastid function), where the top hit is to the sister heterokont group (e.g. hit to oomycetes when diatoms are query sequences). The query genome in each case is shown in the upper right corner of the plot. Broken lines represent quadratic and solid lines linear regressions with adjacent R² values shown. In genes most similar between the heterokont sister groups, there is no apparent phylogenetic signal from red algae in either oomycete or diatom genomes; that is, hits to reds do not deviate positively from the value predicted by the regression model. B. Conversely, with oomycetes removed from the analysis, a regression on top hits versus group size clearly shows a positive signal for red algal genes. This same pattern was found in regressions on top hits against group size for all groups present (Additional file 2, Table 5). Contrary to predictions of the chromalveolate hypothesis, these comparative analyses indicate that the clearly detectable red algal signal in diatom genomes is not present in genes specifically shared with oomycetes.

Figure 3

Distributions of all hits from eukaryotic groups to each heterokont genome. Number of times each designated group is the first to be hit in BLAST searches, through the number of times it yields the sixth hit, are shown from back to front of each graph. Clockwise from the upper left, panels show P. ramorum, Thalassiosira, Phaeodactylum and P. sojae. In each case, defined groups appear in rank order of database size from left to right. The exception is the sister heterokont group, which is shown inset and next to amoebozoans, the unrelated control group with the nearest-sized database.