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Developing Genomic Resources for the Toxic Dinoflagellate Alexandrium tamarense

This study is an integrated, collaborative effort that relies on expertise in molecular evolution and genomics (Debashish Bhattacharya), high quality cDNA library construction (Debashish Bhattacharya, Marcelo Bento Soares), an established Expressed sequence tag (EST) sequencing and bioinformatics pipeline (Marcelo Bento Soares, Debashish Bhattacharya), and expertise in the physiology and culture of Alexandrium tamarense and studies of toxin production (Donald Anderson). This study will result in a valuable molecular resource for scientists working to understand the ecology and toxicity of Harmful algal bloom (HAB) species like Alexandrium tamarense and will provide the detailed insights into the genome of these fascinating protists.

Grant press release [PDF]

Specific Aims

  1. Phylogenomic pipelineTo use phylogenomic and phylogenetic approaches with the Alexandrium tamarense genome data.

  2. To generate a comprehensive unigene set for Alexandrium tamarense using serially subtracted libraries enriched for rare mRNAs.

  3. HeatmapTo generate a transcriptome tag database for Alexandrium tamarense.

    • Massively Parallel Signature Sequencing (MPSS), which allows the generation of gene expression data via acquisition of transcriptome tags, will be used to examine Alexandrium tamarense cDNAs isolated under four different growth conditions (nutrient−repleted, nitrate−depleted, phosphate−depleted and a synchronized culture in G1 producing toxin). A total of at least 350,000 tags will be collected from each condition and identified by comparison to the EST data. Genes that are uniquely expressed within the MPSS data sets under different nutrients conditions or life−history stages will be identified as possible candidate genes that are involved in these functions (e.g., toxin production, nutrient uptake).

Last modified $Date: 2009/06/28 01:08:46 $
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