title: Insights into a dinoflagellate genome through expressed sequence tag analysis.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA. jeremiah-hackett@uiowa.edu
authors.forename: Jeremiah D
authors.initials: JD
authors.lastname: Hackett
authors.forename: Todd E
authors.initials: TE
authors.lastname: Scheetz
authors.forename: Hwan Su
authors.initials: HS
authors.lastname: Yoon
authors.forename: Marcelo B
authors.initials: MB
authors.lastname: Soares
authors.forename: Maria F
authors.initials: MF
authors.lastname: Bonaldo
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Casavant
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016000:Cluster Analysis; D003062:Codon; D019295:Computational Biology / Q000379:methods; D004260:DNA Repair; D018076:DNA, Complementary / Q000378:metabolism; D030541:Databases, Genetic; D004141:Dinoflagellida / Q000235:genetics*; D020224:Expressed Sequence Tags; D005786:Gene Expression Regulation; D015723:Gene Library; D016678:Genome; D023281:Genomics / Q000379:methods*; D006657:Histones / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D018087:Plastids / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D003062:Codon; D018076:DNA, Complementary; D006657:Histones; D012333:RNA, Messenger