About plantiSMASH#

plantiSMASH allows the rapid genome-wide identification, annotation, and analysis of specialized metabolite biosynthetic gene clusters (BGCs) across the plant kingdom. It is a specialized extension of the widely used antiSMASH tool, tailored specifically to target plant genomes.

News#

Version 2.0-beta of plantiSMASH is live now!
plantiSMASH is an extension of the widely used tool antiSMASH, now optimized for and made to work on plant genomes.
plantiSMASH version 2.0-beta features a range of updates and improvements in the areas of gene cluster identification, homology detection, and substrate prediction:

plantiSMASH provides:

• Specific library of pHMM models and completely novel cluster calling logic designed to work on plant genomes
• Specific plant clusterblast database from precalculated plant biosynthetic gene clusters
• Specific training model for gene finding using glimmerHMM
• Homology based metabolic modeling
• Coexpression analysis and html-based visualization on detected biosynthetic gene clusters with the CoExpress module

To top it off, these are the added features of plantiSMASH ver 2.0-beta:

• Updated library of pHMM models and the number of detection rules increased from 6 to 12, including 3 rules being updated.
• Updated plant clusterblast database with precalculated plant biosynthetic gene clusters for 382 NCBI plant genomes.
• Updated specific module for detection of repeats in BURP domains for candidate cyclopeptide BGCs.
• Implemented prediction of substrate specificities of enzyme subfamilies for cellulose synthases, UDP-glucuronosyltransferases, short-chain dehydrogenases, and oxidosqualene cyclases.

Dependencies#

plantiSMASH is powered by several open-source tools:

• NCBI BLAST+
• Diamond
• HMMer 3
• Muscle 3
• GlimmerHMM
• CD-HIT
• PySVG
• JQuery SVG
• JQuery DataTables
• InCHlib
• vis.js
• pplacer
• GraPhlAn

plantiSMASH 2.0 contributors#

plantiSMASH version 2.0 is the product of a collaborative effort between:

• Bioinformatics Group, Wageningen University & Research
• Department of Metabolic Biology, John Innes Centre, Norwich
• The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem
• DOE Joint Genome Institute, Lawrence Berkeley National Labs

Supported by the Graduate School for Experimental Plant Sciences (EPS) and Vidi Grant VI.Vidi.213.183 from The Netherlands Organization for Scientific Research (NWO).

plantiSMASH 1.0 contributors#

plantiSMASH version 1.0 was the product of a collaborative effort between:

• Bioinformatics Group, Wageningen University & Research
• Department of Informatics Engineering, Lampung University
• Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
• Department of Metabolic Biology, John Innes Centre, Norwich

Supported by the Graduate School for Experimental Plant Sciences (EPS),
VENI Grant (#863.15.002) from The Netherlands Organization for Scientific Research (NWO),
a Novo Nordisk Foundation Grant,
UK Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Grant
"Understanding and Exploiting Plant and Microbial Metabolism" (BB/J004561/1),
the John Innes Foundation,
the joint Engineering and Physical Sciences Research Council/BBSRC-funded
OpenPlant Synthetic Biology Research Centre grant BB/L014130/1,
and a National Institutes of Health Genome to Natural Products Network award U101GM110699.

How to cite#

If you have found plantiSMASH useful, please cite:

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters.
Satria A. Kautsar, Hernando G Suarez Duran, Kai Blin, Anne Osbourn & Marnix H. Medema Nucleic Acids Research, 45(W1), W55-W63. (2017) https://doi.org/10.1093/nar/gkx305