Present address: The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, Brisbane, QLD 4072, Australia.
ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE1
Article first published online: 19 JUN 2012
© 2012 Phycological Society of America
Journal of Phycology
Volume 48, Issue 5, pages 1130–1142, October 2012
How to Cite
Chan, C. X., Soares, M. B., Bonaldo, M. F., Wisecaver, J. H., Hackett, J. D., Anderson, D. M., Erdner, D. L. and Bhattacharya, D. (2012), ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE. Journal of Phycology, 48: 1130–1142. doi: 10.1111/j.1529-8817.2012.01194.x
Received 1 August 2011. Accepted 27 February 2012.
- Issue published online: 4 OCT 2012
- Article first published online: 19 JUN 2012
- Accepted manuscript online: 19 MAY 2012 10:46AM EST
- eukaryote evolution;
- horizontal gene transfer;
Microbial eukaryotes may extinguish much of their nuclear phylogenetic history due to endosymbiotic/horizontal gene transfer (E/HGT). We studied E/HGT in 32,110 contigs of expressed sequence tags (ESTs) from the dinoflagellate Alexandrium tamarense (Dinophyceae) using a conservative phylogenomic approach. The vast majority of predicted proteins (86.4%) in this alga are novel or dinoflagellate-specific. We searched for putative homologs of these predicted proteins against a taxonomically broadly sampled protein database that includes all currently available data from algae and protists, and reconstructed a phylogeny from each of the putative homologous protein sets. Of the 2,523 resulting phylogenies, 14%–17% are potentially impacted by E/HGT involving both prokaryote and eukaryote lineages, with 2%–4% showing clear evidence of reticulate evolution. The complex evolutionary histories of the remaining proteins, many of which may also have been affected by E/HGT, cannot be interpreted using our approach with currently available gene data. We present empirical evidence of reticulate genome evolution that combined with inadequate or highly complex phylogenetic signal in many proteins may impede genome-wide approaches to infer the tree of microbial eukaryotes.