Investigating Lipid and Secondary Metabolisms in Plants by Next-generation Sequencing

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.