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.