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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 484.
Published online Oct 20, 2009. doi:  10.1186/1471-2164-10-484
PMCID: PMC2770532
Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?
John W Stiller,corresponding author1 Jinling Huang,1 Qin Ding,2 Jing Tian,2 and Carol Goodwillie1
1Department of Biology, East Carolina University, Greenville, USA
2Department of Computer Science, East Carolina University, Greenville, USA
corresponding authorCorresponding author.
John W Stiller: stillerj/at/ecu.edu; Jinling Huang: huangj/at/ecu.edu; Qin Ding: dingq/at/ecu.edu; Jing Tian: jt0831/at/ecu.edu; Carol Goodwillie: goodwilliec/at/ecu.edu
Received January 28, 2009; Accepted October 20, 2009.
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.
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