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

BMC Genomics

Research Article

Juan F Saldarriaga¹  Patrick J Keeling²  Shehre Banoo Malik³  Claudio H Slamovits³  Renny Lee⁴  Hugo Lai⁴ 

[1] Botany Department, University of British Columbia, V6T1Z4, Vancouver, BS, Canada;Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Alberta, Canada;Botany Department, University of British Columbia, V6T1Z4, Vancouver, BS, Canada;Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Alberta, Canada;Department of Biochemistry and Molecular Biology, Dalhousie University, B3H4R2, Halifax, NS, Canada;Department of Biochemistry and Molecular Biology, Dalhousie University, B3H4R2, Halifax, NS, Canada;

关键词: Dinoflagellates;    Alveolates;    Chromatin;    Genome;    Oxyrrhis;   

DOI  :  10.1186/1471-2164-15-122

 received in 2013-05-19, accepted in 2014-02-06,  发布年份 2014

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Lee et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.