Table 1. Types and rates of SM gene cluster variants in Aspergillus fumigatus strains.

Description	Phenotype	Drivers	Frequency at cluster level	Frequency at strain level	Previous reports
Single-nucleotide polymorphisms and indels	Potential for protein function change (missense); abrogation of protein function (nonsense and frameshift)	DNA replication errors; relaxation of purifying selection	100% (33/33 clusters; missense); 70% (23/33 clusters; nonsense and frameshift)	Every strain affected	Bikaverin in Botrytis [17,27], aflatoxin in A. oryzae and A. flavus [26], fumonisins in Fusarium [10], many others
Gene content polymorphisms	Loss of gene cluster function; structural changes in the metabolite; change in cluster expression or metabolite transport	Deletion and insertion events; recombination; transposable elements	6 clusters	27/66 strains	Trichothecene in Fusarium, aflatoxin and sterigmatocyst in Aspergillus [11–15], HC toxin in Cochliobolus carbonarum [33]
Whole gene cluster polymorphisms	Loss or gain of novel metabolites	Deletion and insertion events; horizontal gene transfer; transposable elements	6 clusters	13/66 strains	Gibberellin and fumonisin in Fusarium [24,25]
Cluster idiomorphs	Changes in metabolites produced or structure of metabolites	Transposable elements; recombination; other mechanisms?	1 gene cluster	8 unique identified alleles	Putative SM gene clusters in dermatophytes; putative SM gene cluster in A. flavus and A. oryzae [34,35]
Mobile gene clusters	Potential for change in gene regulation	Transposable elements; horizontal gene transfer; other mechanisms?	2 gene clusters	8/66 strains	None

Abbreviation: SM; secondary metabolite.