Insights into a dinoflagellate genome through expressed sequence tag analysis.

Jeremiah D. Hackett, Todd E. Scheetz, Hwan Su Yoon, Marcelo B. Soares, Maria F. Bonaldo, Thomas L. Casavant, Debashish Bhattacharya

Research output: Contribution to journalArticle

Abstract

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. 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. 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.

Original languageEnglish (US)
Article number80
JournalBMC Genomics
Volume6
StatePublished - 2005
Externally publishedYes

Fingerprint

Dinoflagellida
Expressed Sequence Tags
Sequence Analysis
Genome
Poisons
Histones
Plastids
Genes
Harmful Algal Bloom
DNA Packaging
Chloroplast Proteins
Double-Stranded DNA Breaks
Nucleosomes
Nucleic Acid Databases
Base Composition
Eukaryota
Gene Library
Codon
Organelles
Cell Biology

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Hackett, J. D., Scheetz, T. E., Yoon, H. S., Soares, M. B., Bonaldo, M. F., Casavant, T. L., & Bhattacharya, D. (2005). Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics, 6, [80].

Insights into a dinoflagellate genome through expressed sequence tag analysis. / Hackett, Jeremiah D.; Scheetz, Todd E.; Yoon, Hwan Su; Soares, Marcelo B.; Bonaldo, Maria F.; Casavant, Thomas L.; Bhattacharya, Debashish.

In: BMC Genomics, Vol. 6, 80, 2005.

Research output: Contribution to journalArticle

Hackett, JD, Scheetz, TE, Yoon, HS, Soares, MB, Bonaldo, MF, Casavant, TL & Bhattacharya, D 2005, 'Insights into a dinoflagellate genome through expressed sequence tag analysis.', BMC Genomics, vol. 6, 80.
Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL et al. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics. 2005;6. 80.
Hackett, Jeremiah D. ; Scheetz, Todd E. ; Yoon, Hwan Su ; Soares, Marcelo B. ; Bonaldo, Maria F. ; Casavant, Thomas L. ; Bhattacharya, Debashish. / Insights into a dinoflagellate genome through expressed sequence tag analysis. In: BMC Genomics. 2005 ; Vol. 6.
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