Abstract
BackgroundThe 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.ResultsWe 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.ConclusionThe 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.
Highlights
The alveolates include a large number of important lineages of protists and algae, among which are three major eukaryotic groups: ciliates, apicomplexans and dinoflagellates
Visual inspection of the clusters revealed that a large number of the short clusters were low complexity repeats, we decided to discard all sequences shorter than 200 bases in order to prioritize the quality of the data, resulting in a final set of 8,141 clusters
We tapped on this valuable dataset to conduct additional investigations, this time concentrating on genes and molecular characteristics associated to nuclear and genomic biology, which is an area where dinoflagellates are unusual
Summary
The alveolates include a large number of important lineages of protists and algae, among which are three major eukaryotic groups: ciliates, apicomplexans and dinoflagellates. O. marina is well suited to explore the origins and the unusual characteristics of two important groups of protists, dinoflagellates and apicomplexans In this regard, Oxyrrhis represents an early branch within the Dinoflagellates are known for their highly divergent features, such as expansive genomes, an unusual karyokinetic process and a very atypical chromatin structure, unique among eukaryotes [6,7,8,9,10]. O. marina is a robust organism that is easy to maintain in the laboratory; it grows fast and has flexible nutritional requirements [11,12] These advantages explain in part why O. marina is a fashionable model organism, but lack of molecular data has been a severe limitation to the scope of questions that can be addressed with this species
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