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

doi:10.1186/1471-2164-6-80

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Insights into a dinoflagellate genome through expressed sequence tag analysis

Journal article

Open access

Peer reviewed

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 and Debashish Bhattacharya

BMC genomics, Vol.6(1), pp.80-80

05/29/2005

DOI: 10.1186/1471-2164-6-80

PMCID: PMC1173104

PMID: 15921535

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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.

Amino Acid Sequence

Computational Biology - methods

Gene Library

Gene Expression Regulation

Databases, Genetic

Molecular Sequence Data

Phylogeny

RNA, Messenger - metabolism

Sequence Homology, Amino Acid

Dinoflagellida - genetics

Animals

Codon

DNA Repair

Plastids - metabolism

Histones - metabolism

Genome

Genomics - methods

DNA, Complementary - metabolism

Cluster Analysis

Expressed Sequence Tags

Details

Title: Subtitle: Insights into a dinoflagellate genome through expressed sequence tag analysis
Creators: Jeremiah D Hackett - Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA. jeremiah-hackett@uiowa.edu
Todd E Scheetz
Hwan Su Yoon
Marcelo B Soares
Maria F Bonaldo
Thomas L Casavant
Debashish Bhattacharya
Resource Type: Journal article
Publication Details: BMC genomics, Vol.6(1), pp.80-80
DOI: 10.1186/1471-2164-6-80
PMID: 15921535
PMCID: PMC1173104
NLM abbreviation: BMC Genomics
ISSN: 1471-2164
eISSN: 1471-2164
Publisher: England
Grant note: R01 GM098629 / NIGMS NIH HHS T 32 GM98629 / NIGMS NIH HHS
Language: English
Date published: 05/29/2005
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Ophthalmology and Visual Sciences
Record Identifier: 9983979952702771

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