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MBE Advance Access published online on December 15, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj075
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted December 12, 2005

Research Article

Phylogenomic Analysis Identifies Red Algal Genes of Endosymbiotic Origin in the Chromalveolates

Shenglan Li 1 1, Tetyana Nosenko 1 1, Jeremiah D. Hackett 2, and Debashish Bhattacharya 1 *

1 Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, Iowa 52242, United States
2 Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, 446 Biology Building, Iowa City, Iowa 52242, United States; Present address: Biology Department, Woods Hole Oceanographic Institution, Mail Stop #32, Woods Hole, MA 02543, USA

* To whom correspondence should be addressed.
Debashish Bhattacharya, E-mail: debashi-bhattacharya{at}uiowa.edu


  Abstract

Endosymbiosis has spread photosynthesis to many branches of the eukaryotic tree however the history of photosynthetic organelle (plastid) gain and loss remains controversial. Fortuitously, endosymbiosis may leave a genomic footprint through the transfer of endosymbiont genes to the "host" nucleus (endosymbiotic gene transfer, EGT). EGT can be detected through comparison of host genomes to uncover the history of past plastid acquisitions. Here we focus on a lineage of chlorophyll c-containing algae and protists ("chromalveolates") that are postulated to share a common red algal secondary endosymbiont. This plastid is originally of cyanobacterial origin through primary endosymbiosis and is closely related among the Plantae (i.e., red, green, and glaucophyte algae). To test these ideas, an automated phylogenomics pipeline was used with a novel uni-gene data set of 5,081 expressed sequence tags (ESTs) from the haptophyte alga Emiliania huxleyi and genome or EST data from other chromalveolates, red algae, plants, animals, fungi and bacteria. We focused on nuclear-encoded proteins that are targeted to the plastid to express their function because this group of genes is expected to have phylogenies that are relatively easy to interpret. A total of 708 genes were identified in E. huxleyi that had a significant BLAST hit to at least one other taxon in our data set. Forty-six of the alignments that were derived from the 708 genes contained at least one other chromalveolate (i.e., besides E. huxleyi), red and/or green algae (or land plants), and one or more cyanobacteria, whereas 15 alignments contained E. huxleyi, one or more other chromalveolates, and only cyanobacteria. Detailed phylogenetic analyses of these data sets turned up 19 cases of EGT that did not contain significant paralogy and had strong bootstrap support at the internal nodes, allowing us to confidently identify the source of the plastidtargeted gene in E. huxleyi. A total of 17 genes originated from the red algal lineage, whereas 2 genes were of green algal origin. Our data demonstrate the existence of multiple red algal genes that are shared among different chromalveolates suggesting that at least a subset of this group may share a common origin.

Keywords: chromalveolates; Emiliania huxleyi; endosymbiosis; gene transfer; phylogenomics.

1These authors have contributed equally to the manuscript.


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