Table 1 |.

Tools and techniques for mining the fungal secondary metabolome

Genetic and Bioinformatic tool	Feature	Refs
Endogenous expression systems
Targeted promoter exchange	Synthetic promoter	99
Transcription factor OE	Synthetic promoter	50,118,149
Epigenetic remodelling	Chromatin in repressed state	58,60,62–66,147,148,151–153
Global regulator OE	Synthetic promoter	55,119
Expression methods for heterologous hosts
Yeast stitching	Synthetic BGC, universal host	122
FAC	Scalable expression in Aspergillus	12
CoIN	Co-induction of sterigmatocystin promoters	154
Hex	Scalable expression in Saccharomyces	125
BGC mining algorithms
SMURF	Synthases (NRPS, PKS, DMATS and NRPS–PKS) and coordinates of genes	112
AntiSMASH	Synthases and substrate predictors	155
PRISM	NRPS, PKS and NRPS–PKS dereplication	156
SMIPS and CASSIS	DNA regulatory site	157
MIDDAS	Gene annotation, proteins and transcriptome data	18
FunGeneClusterS	NRPS, PKS, DMATS and co-expression data	158
SeMPI	Modular PKS	159
DEREPLICATOR+	Dereplication strategies	117
Databases with fungal and bacterial BGCs
ClusterMine360	297 BGCs	160
IMG-ABC	2,489 BGCs	161
MIBiG	1,393 BGCs	109
Substrate predictors
AntiSMASH	Incorporates NRPS predictor	161
NP.searcher	Bacteria, output chemical structure	100
Pep2Path	MassSpec guided peptidic natural products	162
PRISM	NRPS, PKS and NRPS–PKS dereplication	156
GRAPE	Works with PRISM, retrobiosynthesis PKs and NRPs	163
GARLIC	Compares PRISM and GRAPE outputs for likelihood of backbone prediction	163
SeMPI	Modular PKS	159
NRPS predictor	A domain specificity	164

BGC, biosynthetic gene cluster; CASSIS, cluster assignment by islands of sites; CoIN, co-inducible nitrate; DMATS, dimethylallyl tryptophan synthase; FAC, fungal artificial chromosome; NRP, non-ribosomal peptide; NRPS, non-ribosomal peptide synthetase; OE, overexpression; PK; polyketide; PKS, polyketide synthase; SMIPS, secondary metabolites by InterProScan.