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

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    Article (150.9Kb)
    Supplemental material (83.25Kb)
    Date
    2006-01
    Author
    Dyhrman, Sonya T.  Concept link
    Haley, Sheean T.  Concept link
    Birkeland, Shanda R.  Concept link
    Wurch, Louie L.  Concept link
    Cipriano, Michael J.  Concept link
    McArthur, Andrew G.  Concept link
    Metadata
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    Citable URI
    https://hdl.handle.net/1912/414
    As published
    https://doi.org/10.1128/AEM.72.1.252-260.2006
    DOI
    10.1128/AEM.72.1.252-260.2006
    Abstract
    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 serial analysis of gene expression (SAGE) 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 twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (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 (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) 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.
    Description
    Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 252-260, doi:10.1128/AEM.72.1.252-260.2006.
    Collections
    • Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
    • Biology
    Suggested Citation
    Applied and Environmental Microbiology 72 (2006): 252-260
     
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