Phytochemical Genomics on the Way

This is a really exciting time for phytochemistry research. Plant scientists studying specialized plant metabolism (previously often known as ‘secondary metabolism’) can foresee tremendous advances in their understanding of the mechanisms underlying the production and function of an enormous variety of plant metabolites, and of their regulation and evolution. Such remarkable progress would never have been expected 10 years ago and has taken place in just the last few years (Yonekura-Sakakibara and Saito 2009). Two technological breakthroughs seem to have been the key triggers for this unforeseen progress: metabolomics and mass DNA sequencing. Metabolomics is <15 years old, yet the concept was immediately applied to the plant field as scientists realized its tremendous potential for understanding the capacity of plants for making a huge array of compounds (Bino et al. 2004). Metabolomics now makes possible comprehensive profiling of nearly all the metabolites that accumulate in plant cells (Saito and Matsuda 2010). The second technological breakthrough was ultra-high-throughput DNA sequencing, with so-called ‘next-generation DNA sequencers’ (Wang et al. 2009, Ozsolak and Milos 2011). Until the realization of this technology, no one would have anticipated genomics-based studies of hundreds of medicinal or exotic plant species—genomics was only for model plants or major crops, whose genome sequences could only be revealed by large international research consortia (or by huge well-funded undertakings). However, newly developed mass DNA sequencers have made comprehensive genome and transcriptome sequencing possible for ordinary phytochemical researchers who are investigating the synthesis of particular plant metabolites out of their own curiosity. By combining data sets from metabolomics and genomics/transcriptomics, one can understand relationships between metabolites and genes that allow the generation of testable hypotheses about the functions of genes and metabolites (Higashi and Saito 2013, Hur et al. 2013, Yonekura-Sakakibara et al. 2013). During this integration and hypothesis-generation phase, databases and bioinformatics play indispensable roles in reducing this ‘systems biology’ workload. Such studies will provide us with an understanding of the evolution of genes and pathways and hence in-depth fundamental insights into plant life. This special focus issue (SFI) on ‘Phytochemical Genomics’ is intended to serve as a synthesis of the most up to date information in this field, indicating not only current trends but also its future prospects.