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Open Access Highly Accessed Research article

Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution

Renny Lee2, Hugo Lai2, Shehre Banoo Malik12, Juan F Saldarriaga3, Patrick J Keeling13 and Claudio H Slamovits12*

Author Affiliations

1 Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Alberta, Canada

2 Department of Biochemistry and Molecular Biology, Dalhousie University, B3H4R2 Halifax, NS, Canada

3 Botany Department, University of British Columbia, V6T1Z4 Vancouver, BS, Canada

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BMC Genomics 2014, 15:122  doi:10.1186/1471-2164-15-122

Published: 11 February 2014

Abstract

Background

The alveolates include a large number of important lineages of protists and algae, among which are three major eukaryotic groups: ciliates, apicomplexans and dinoflagellates. Collectively alveolates are present in virtually every environment and include a vast diversity of cell shapes, molecular and cellular features and feeding modes including lifestyles such as phototrophy, phagotrophy/predation and intracellular parasitism, in addition to a variety of symbiotic associations. Oxyrrhis marina is a well-known model for heterotrophic protist biology, and is now emerging as a useful organism to explore the many changes that occurred during the origin and diversification of dinoflagellates by virtue of its phylogenetic position at the base of the dinoflagellate tree.

Results

We have generated and analysed expressed sequence tag (EST) sequences from the alveolate Oxyrrhis marina in order to shed light on the evolution of a number of dinoflagellate characteristics, especially regarding the emergence of highly unusual genomic features. We found that O. marina harbours extensive gene redundancy, indicating high rates of gene duplication and transcription from multiple genomic loci. In addition, we observed a correlation between expression level and copy number in several genes, suggesting that copy number may contribute to determining transcript levels for some genes. Finally, we analyze the genes and predicted products of the recently discovered Dinoflagellate Viral Nuclear Protein, and several cases of horizontally acquired genes.

Conclusion

The dataset presented here has proven very valuable for studying this important group of protists. Our analysis indicates that gene redundancy is a pervasive feature of dinoflagellate genomes, thus the mechanisms involved in its generation must have arisen early in the evolution of the group.

Keywords:
Dinoflagellates; Alveolates; Chromatin; Genome; Oxyrrhis