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Informatics Support for the Emiliania huxleyi Serial Analysis of Gene Expression Project

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Long-SAGE (serial analysis of gene expression) for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

Applied and Environmental Microbiology, in press

Sonya T. Dyhrman1, Sheean T. Haley1, Shanda R. Birkeland2, Louie L. Wurch1, Michael J. Cipriano2, and Andrew G. McArthur2

The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use Long-SAGE (serial analysis of gene expression) to identify E. huxleyi genes responsive to nitrogen (N), or phosphorus (P) starvation. Long-SAGE is an elegant approach for examining quantitative, and comprehensive, gene expression patterns without a priori knowledge of gene sequences via the detection of 21 bp nucleotide sequence tags. E. huxleyi appears to have a robust, transcriptional level response to macronutrient deficiency with 42 tags uniquely present or up-regulated 2 fold or greater in the N starved library and 128 tags uniquely present or up-regulated 2 fold or greater in the P starved library. The expression patterns of several tags were validated with RT-PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or EST sequence data. For example, in the P starved library a number of the tags mapped to genes with a role in P scavenging including a putative phosphate repressible permease and a putative polyphosphate synthetase. In short, the Long-SAGE analyses have 1) identified many new differentially-regulated gene sequences, 2) assigned regulation data to EST sequences with no data-base homology and unknown function, and 3) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our Long-SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.

1Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA

2Marine Biological Laboratory, Woods Hole, MA

Summary Statistics

Total Number of Contigs8,635
Total Number of Supercontigs8,635
Average Shotgun Coverage1.00
Estimated Closure (of two hundred fourty Mbp)3.48%
Predicted Open Reading Frames3,497
Transcribed ORFs (SAGE detection)1,215
Number of SAGE Libraries4
Number of Unique SAGE Tags (filtered)7,864
SAGE Tags mapped to ORFs1,677
Statistics updated every 24 hours.
Detailed statistics: Assembly, ORFs, SAGE




Funding provided by the Woods Hole Oceanographic Institution's Ocean Life Institute


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