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Open Access Research article

Insights into a dinoflagellate genome through expressed sequence tag analysis

Jeremiah D Hackett1, Todd E Scheetz2, Hwan Su Yoon1, Marcelo B Soares34, Maria F Bonaldo3, Thomas L Casavant5 and Debashish Bhattacharya1*

Author Affiliations

1 Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA

2 Department of Ophthalmology and Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA 52242, USA

3 Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA

4 Departments of Biochemistry, Orthopaedics, Physiology, and Biophysics, University of Iowa, Iowa City, IA 52242, USA

5 Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA

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BMC Genomics 2005, 6:80  doi:10.1186/1471-2164-6-80

Published: 29 May 2005

Abstract

Background

Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging.

Results

Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair.

Conclusion

This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.