Plants synthesize an enormous variety of organic compounds, either directly (primary metabolites) or indirectly (secondary metabolites) involved in in growth and development (Buchanan et al. 2000). Colouring pigments such as carotenoids and flavonoids, fragrance enhancing aromatic molecules, and phytonutrients such as phytic acid, ascorbic acid (Vitamin C), and tocopherol are some examples of phytochemicals. Primary metabolites perform metabolic roles that are essential for any plant. Primary metabolites are for instance the amino acids, acyl lipids, organic acids, sugars, nucleotides, and phytosterols that are found in all plants. Secondary metabolites, or natural compounds, are often species of family specific and less widespread in the plant kingdom. They can be specific for a taxonomic group, such as capsaicinoids, found in Capsicum species, and caffeine, that is only found in a few species, like Coffee (Coffea spp), tea (Camellia sinensis), kola nut (Cola nitida), guarana (Paullinia cupana), holly maté  (Ilex paraguariensis) and cacao (Theobroma cacao) (Silvarolla et al. 2004; Ishida et al. 2009; Crown et al. 2012). Glucosinolates, which are cruciferous (brassica) specific compounds that are connected with cancer prevention, are another example (Shapiro et al. 1998).

Likely over 200,000 different secondary metabolites exist in the plant kingdom, and each species, and cultivar/genotype has its own mixture (Keurentjes et al. 2006). Based on their biosynthesis, the majority of secondary metabolites can be divided into three main chemical classes: the terpenoids, alkaloids and phenolic compounds. Initially, these compounds were thought to be waist products of primary metabolism and therefore deemed biologically unimportant, hence their name; secondary metabolites. However, they received much attention from organic chemists, stimulating the development of a branch of science that is now known as organic chemistry. Interest for natural compounds was through their great utility as flavouring agents, perfumes, drugs, dyes, glues, oils, polymers, fibres, and waxes. Growing appreciation and applications has renewed research in this field, and the possible natural roles of these compounds in plants are being studied, especially in the context of ecological interactions. Plants attract pollinating insects and birds, as well as seed-dispersing animals. They can also repel herbivores or attract microorganisms. Renewed interest for these compounds is also fuelled by the search for new antibiotics, drugs, insecticides, UV-protectants, and herbicides. Finally, many quality attributes of plant-derived food, such as colour, flavour and fragrance are based on secondary metabolites. We will now briefly introduce the secondary metabolites that will be discussed throughout this document, the carotenoids, the flavonoids, the vitamins tocopherol (Vitamin E), and ascorbic acid (Vitamin C), and phytic acid. 


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