Genomic identification and analysis of specialized metabolite biosynthetic gene clusters in plants using plantiSMASH

Plants produce a vast diversity of specialized metabolites, which play important roles in the interactions with their microbiome, as well as with animals and other plants. Many such molecules have valuable biological activities that render them (potentially) useful as medicines, flavors and fragrances, nutritional ingredients, or cosmetics. Recently, plant scientists have discovered that the genes for many biosynthetic pathways for the production of such specialized metabolites are physically clustered on the chromosome within biosynthetic gene clusters (BGCs). The Plant Secondary Metabolite Analysis Shell (plantiSMASH) allows for the automated identification of such plant BGCs, facilitates comparison of BGCs across genomes, and helps users to predict the functional interactions of pairs of genes within and between BGCs based on coexpression analysis. In this chapter, we provide a detailed protocol on how to install and run plantiSMASH, and how to interpret its results to draw biological conclusions that are supported by the data.</p

Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae

Differentiation of secondary metabolite profiles in closely related plant species provides clues for unravelling biosynthetic pathways and regulatory circuits, an area that is still underinvestigated. Cucurbitacins, a group of bitter and highly oxygenated tetracyclic triterpenes, are mainly produced by the plant family Cucurbitaceae. These compounds have similar structures, but differ in their antitumour activities and ecophysiological roles. By comparative analyses of the genomes of cucumber, melon and watermelon, we uncovered conserved syntenic loci encoding metabolic genes for distinct cucurbitacins. Characterization of the cytochrome P450s (CYPs) identified from these loci enabled us to unveil a novel multi-oxidation CYP for the tailoring of the cucurbitacin core skeleton as well as two other CYPs responsible for the key structural variations among cucurbitacins C, B and E. We also discovered a syntenic gene cluster of transcription factors that regulates the tissue-specific biosynthesis of cucurbitacins and may confer the loss of bitterness phenotypes associated with convergent domestication of wild cucurbits. This study illustrates the potential to exploit comparative genomics to identify enzymes and transcription factors that control the biosynthesis of structurally related yet unique natural products.National Key R &amp; D Program for Crop Breeding [2016YFD0100307]; National Science Fund for Distinguished Young Scholars [31225025]; National Program on Key Basic Research Projects in China (the 973 Program) [2012CB113900]; leading talents of Guangdong province Program [00201515]; National Natural Science Foundation of China [31322047, 31401886, 31101550, 31672171]; Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS); Chinese Ministry of Finance [1251610601001]; China Postdoctoral Science Foundation [2014M550902]; Discovery Grant from National Science and Engineering Research Council of Canada (NSERC); Canada Research Chair program; UK Biotechnological and Biological Sciences Research Council Institute Strategic Programme Grant &apos;Understanding and Exploiting Plant and Microbial Metabolism&apos; [BB/J004561/1]; John Innes Foundation; Genomes to Natural Products National Institutes of Health Programme [U01GM110699]; Shenzhen Municipal Government; Dapeng District GovernmentSCI(E)[email protected]; [email protected]