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Background  The biosynthesis of aflatoxin (AF) involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST) and  O -methylsterigmatocystin (OMST), the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are  A .  nidulans  that synthesizes only ST,  A .  flavus  that makes predominantly AF, and  A .  parasiticus  that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of  Aspergillus .    Results  To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five  Aspergillus  genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs ( aflA/aflB, aflR/aflS, aflX/aflY ,  aflF/aflE, aflT/aflQ ,  aflC/aflW , and  aflG/aflL ). With the exception of  A. nomius , contrasts of mean  Ka/Ks  values across all cluster genes showed significant differences in selective pressure between section  Flavi  and non-section  Flavi  species.  A. nomius  mean  Ka/Ks  values were more similar to partial clusters in  A. fumigatus  and  A. terreus . Overall, mean  Ka/Ks  values were significantly higher for section  Flavi  than for non-section  Flavi  species.    Conclusion  Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy ( aflF / aflE ) or the copies may partition the ancestral function ( aflA/aflB ). In some gene modules, the duplicated copy may simply augment/supplement a specific pathway function ( aflR/aflS  and  aflX/aflY ) or the duplicated copy may evolve a completely new function ( aflT/aflQ  and  aflC/aflW ). Gene modules that are contiguous in one species and noncontiguous in others point to possible rearrangements of cluster genes in the evolution of these species. Significantly higher mean  Ka/Ks  values in section  Flavi  compared to non-section  Flavi  species indicate increased positive selection acting in the evolution of genes in OMST and AF gene clusters.

Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster