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Title: Investigating Lipid and Secondary Metabolisms in Plants by Next-generation Sequencing
Keywords: Lipid, Secondary metabolism, Next-generation sequencing
Issue Date: 23-Jul-2014
Citation: JIN JINGJING (2014-07-23). Investigating Lipid and Secondary Metabolisms in Plants by Next-generation Sequencing. ScholarBank@NUS Repository.
Abstract: Plant metabolites are compounds synthesized by plants for essential and specific functions (primary metabolites and secondary metabolites). Next-generation sequencing (NGS) techniques have been proved valuable in the investigation of different plant metabolisms. We first develop a reference-based genome assembly pipeline, including mis-assembled and repeat scaffold identification components. Next, we use this pipeline to construct a draft genome for Dura oil palm. By resequencing 12 different oil palm strains, around 21 million high-quality SNPs are found. Moreover, a GBrowse-based database with a BLAST tool is developed to visualize different genome information of oil palm. In order to predict new functions/metabolisms for plants, a weighted pathway approach is proposed, which tries to consider dependencies between different pathways. After applying this approach to an RNA-seq dataset from spearmint, several new functions and metabolisms are uncovered, which is consistent with GC-MS results and by q-PCR experiment.
Appears in Collections:Ph.D Theses (Open)

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