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

Satria A. Kautsar, Hernando G. Suarez Duran, Marnix H. Medema*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

5 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationPlant Chemical Genomics
Subtitle of host publicationMethods and Protocols
EditorsFriedrich Fauser, Martin Jonikas
Place of PublicationNew York
PublisherHumana Press Inc.
ISBN (Electronic)9781493978748
ISBN (Print)9781493978731
Publication statusPublished - 31 May 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Bioinformatics
  • Biosynthetic gene cluster
  • Biosynthetic pathway
  • Genomic
  • Plant
  • Secondary metabolite
  • Specialized metabolite


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