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Developing Genomic Resources for the Toxic Dinoflagellate
Alexandrium tamarense

(Funded by NIH: NIEHS R01 ES013679-01A2)
 
 

STATEMENT
image of alexandrium tamarense Alexandrium tamarense (At) is a unicellular protist that causes harmful algal blooms (HABs) and paralytic shellfish poisoning. The impacts of HABs on marine ecosystems and the seafood industry are substantial. A recent study estimated the average economic impact in the United States from HABs between 1987-1992 to be 49 million dollars a year, including 18 million in damage to commercial fisheries. This figure does not include loss of potential income generated by the vast shellfish resources in Alaska and Georges Bank that are closed because of paralytic shellfish poisoning caused by At. In addition, the saxitoxins produced by At are suspected as a cause of mortality in sea birds and humpback whales and human intoxication and death. Very little is known, however, about the factors that influence the formation of HABs or their recent spread to new areas. A critical requirement for controlling At is knowledge about its basic biology and toxin production, areas of research that will be significantly aided by the availability of a genomic resource for this species. Characterization of At will also shed light into genome evolution in dinoflagellates, taxa that are renowned for their ability to incorporate multiple endosymbionts and to accumulate foreign genes through horizontal gene transfer (HGT).
This proposal is an integrated, collaborative effort that relies on expertise in molecular evolution and genomics (Debashish Bhattacharya), high quality cDNA library construction (D. Bhattacharya, M. Bento Soares), an established expressed sequence tag (EST) sequencing and bioinformatics pipeline (M.B. Soares, D. Bhattacharya), and expertise in the physiology and culture of At and studies of toxin production (Don Anderson). This study will result in a valuable molecular resource for scientists working to understand the ecology and toxicity of HAB species like At and will provide the detailed insights into the genome of these fascinating protists.


A. SPECIFIC AIMS

Our specific aims are to use a highly efficient gene discovery strategy to generate a comprehensive EST unigene set for At to determine the extent of lateral gene transfer in this species. We will also use massively parallel signature sequencing (MPSS) analysis to create a transcriptome tag database for At cells grown in different culture conditions that affect nutrient physiology, cell and life cycle stages, and toxin production.
 
 
Aim 1.
To generate a comprehensive uni-gene set for Alexandrium using serially subtracted libraries enriched
for rare mRNAs.
 
   

We will construct a non-normalized cDNA library from At that is derived from pooled cDNA isolated from cells that are:
1) nitrate-depleted, 2) phosphate-depleted, 3) generating newly-formed cysts, 4) germinating cysts, 5) synchronized in G1 phase, and 6) in the middle of the dark period. A total of 1,000 ESTs will be sequenced at the 3’ terminus from this library to identify highly expressed genes. Thereafter, unique cDNAs that have already been generated using a nutrient-replete culture of At (8,996 ESTs) will be used as a driver to subtract from the pooled cDNA library. A total of 9,000 cDNAs in the subtracted library will be sequenced at the 3’ terminus. These EST data will be made freely available to the scientific community with a dedicated web server in the Bhattacharya lab (http://www.biology.uiowa.edu/debweb/AlexandriumEST/) and will also be released on a weekly basis to GenBank (dbEST; http://www.ncbi.nlm.nih.gov/dbEST/) to facilitate the broadest distribution. Until now, a total of 10,885 At ESTs have been released to dbEST.

 
 
Aim 2.
To use phylogenomic and phylogenetic approaches with the At genome data.
 
   

A phylogenomic pipeline that has been established in the Bhattacharya lab will be used to analyze the genome data from At to determine the contribution of horizontal and endosymbiotic gene transfer to nuclear genome evolution in this species.

 
 
Aim 3.
To generate a transcriptome tag database for Alexandrium.
 
   

MPSS, which allows the generation of gene expression data via acquisition of transcriptome tags, will be used to examine At cDNAs isolated under 4 different growth conditions (nutrient replete, 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 nutrient conditions or life-history stages will be identified as possible candidate genes that are involved in these functions (e.g., toxin production, nutrient uptake).

 
 
Grant press release
 
 

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