Table 1.
Clustered pathways for the biosynthesis of plant natural products
| Pathway | Class of compound | Plant species | Annual/perennial | Method of cluster discovery | Reference |
|---|---|---|---|---|---|
| Eudicotsa | |||||
| Thalianol (1a–e) | Triterpene | Arabidopsis thaliana | Annual | Cluster mining | Field & Osbourn (2008) |
| Marneral (2a–d) | Triterpene | Arabidopsis thaliana | Cluster mining | Field et al. (2011) | |
| Tirucalla-7,24-dien-3β-ol (3) | Triterpene | Arabidopsis thaliana | Cluster mining | Boutanaev et al. (2015) | |
| Arabidiol (4a–c) | Triterpene | Arabidopsis thaliana | Cluster mining | Castillo et al. (2013); Sohrabi et al. (2015) | |
| Cucurbitacins (5a–e) | Triterpene | Cucumis sativus | Annual | Cluster mining; trait-based discovery (characterization of the Bi locus for bitterness) | Boutanaev et al. (2015); Shang et al. (2014) |
| Casbene diterpenoids (6a–b) | Diterpene | Euphorbia peplus | Annual | Characterized biosynthetic genes to clusteringc | King et al. (2014) |
| Casbene diterpenoids | Diterpene | Jatropha curcas | Perennial | Genome mining; genetics | King et al. (2014) |
| 20-Hydroxybetulinic acid (7) | Triterpene | Lotus japonicus | Annual | Cluster mining | Krokida et al. (2013) |
| Linamarin (8)/lotaustralin (9) | Cyanogenic glycoside | Lotus japonicus | Annual | Isolation of cyanogenesis deficient mutants; genomics | Takos et al. (2011) |
| Linamarin (8)/lotaustralin (9) | Cyanogenic glycoside | Manihot esculenta | Perennial | Characterized biosynthetic genes to cluster | Takos et al. (2011) |
| Noscapine (10) | Benzylisoquinoline alkaloid | Papaver somniferumb | Annual | Trait-based discovery (characterization of High Noscapine 1 locus) | Winzer et al. (2012) |
| Casbene diterpenoids (6a–f) | Diterpene | Ricinus communis | Perennial with annual forms | Cluster mining; characterized biosynthetic genes to cluster | Boutanaev et al. (2015); King et al. (2014) |
| α-Tomatine (11) | Steroidal alkaloid | Solanum lycopersicum | Perennial with annual forms | Characterized biosynthetic genes to cluster | Itkin et al. (2013) |
| α-Chaconine (12)/α-solanine (13) | Steroidal alkaloid | Solanum tuberosum | Perennial | Characterized biosynthetic genes to cluster; synteny with Solanum lycopersicon | Itkin et al. (2013) |
| Monoterpenes (14)/diterpenes (15) | Terpenes | Solanum lycopersicum | Perennial with annual forms | Characterized biosynthetic genes to cluster | Falara et al. (2011); Matsuba et al. (2013, 2015) |
| Monocots | |||||
| Avenacins (16a–d) | Triterpene | Avena strigosab | Annual | Trait-based discovery (forward screen for avenacin-deficient mutants) | Qi et al. (2004, 2006); Mugford et al. (2009, 2013) |
| β-Diketones (18a–c) | Polyketide | Hordeum vulgare | Annual | Trait-based discovery (characterization of the Cer-cqu leaf wax locus) | Schneider et al. (2016) |
| Momilactones (17a, b) | Diterpene | Oryza sativa | Annual | Characterized biosynthetic genes to cluster | Wilderman et al. (2004); Shimura et al. (2007) |
| Phytocassanes (19a–e), oryzalides (20a, b) | Diterpene | Oryza sativa | Annual | Characterized biosynthetic genes to cluster | Swaminathan et al. (2009) |
| Dhurrin (21) | Cyanogenic glycoside | Sorghum bicolor | Annual | Characterized biosynthetic genes to cluster | Takos et al. (2011) |
| 2,4-dihydroxy-7-methoxy-1, 4-benzoxazin-3-one (DIMBOA, 22a–d) | Hydroxamic acid | Zea mays | Annual | Trait-based discovery (screen for bx1 mutants) | Frey et al. (1997); von Rad et al. (2001); Frey et al. (2003); Jonczyk et al. (2008) |
The products of the pathways are shown in Fig. 1.
Species for which genome sequences are not publicly available. Clusters were therefore defined by assembling and sequencing bacterial artificial chromosome (BAC) contigs (Mugford et al., 2009; Mugford et al., 2013; Qi et al., 2006; Winzer et al., 2012).
For casbene diterpene biosynthesis in E. peplus, only two adjacent genes have been discovered so far (a casbene synthase and CYP72A19). Although this region does not contain genes encoding a minimum of three different types of enzymes, it has been included in the table since it emerged from a wider investigation of production of casbene diterpenoids in the wider Euphorbiaceae (see entries for castor (Ricinus communis) and jatropha (Jatropha curcas)) (King et al., 2014).