Figure 2.

Schematic work flow of NGS-guided de novo genome assembly and integrative genome analysis to understand plant metabolism. The high accuracy and coverage of NGS-derived reads allow de novo genome assembly and gene annotation. Integrative genome analyses coupled with transcriptomic and metabolic data sets enable the identification of biosynthetic and regulatory pathways controlling plant metabolism. Commonly used approaches are shown with an example of a study where these approaches were applied. A, Single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) discovery (Chen et al., 2014). B, Structural variant discovery (Da Silva et al., 2013). C, Phylogenetic analysis (Denoeud et al., 2014). D, Network analysis (Itkin et al., 2013). E, Transcriptome analysis (Fu et al., 2013). F, Physical cluster identification (Winzer et al., 2012).