Developing Aiptasia pallida as a tractable model system for cnidarian-dinoflagellate symbiosis : identifying transferred metabolites and designing tools for analysis of ultra-high-throughput-sequencing data
- This dissertation describes a general method for identifying and roughly quantifying the metabolites that are produced by symbiotic dinoflagellates and transferred to cnidarian hosts. I developed a system of rapid filtration and gas chromatography-mass spectrometry (GC-MS) to identify these compounds in the anemone tissue and dinoflagellates separately. I used 13C-sodium bicarbonate to label compounds produced from newly-fixed carbon; the principal compound detected in the animal was glucose. I developed a way to visualize these and other large GC-MS datasets using open-source software. I also built tools for analyzing Ultra-High-Throughput-Sequencing (UHTS) data, and these were useful in the de novo assembly of the Aiptasia pallida transcriptome. One tool I developed compares each read to each other read using a MapReduce framework to merge near-duplicate reads and reduce redundancy in the dataset. In addition, our lab sequenced symbiotic animals and therefore often worked with pools of sequences from multiple organisms. I developed a tool for identifying which transcript sequence was produced by which organism in a symbiotic ecosystem: it was 99% accurate on high-quality validation data.
|Type of resource
|electronic; electronic resource; remote
|1 online resource.
|Burriesci, Matthew Strecker
|Stanford University, Department of Genetics
|Statement of responsibility
|Matthew Strecker Burriesci.
|Submitted to the Department of Genetics.
|Thesis (Ph. D.)--Stanford University, 2011.
- © 2011 by Matthew Strecker Burriesci
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