The filamentous fungi Aspergillus parasiticus and Aspergillus flavus produce the carcinogenic secondary metabolite aflatoxin on susceptible crops. These species differ in the quantity of aflatoxins B 1 , B 2 , G 1 , and G 2 produced in culture, in the ability to produce the mycotoxin cyclopiazonic acid, and in morphology of mycelia and conidiospores. To understand the genetic basis for differences in biochemistry and morphology, we conducted next-generation sequence (NGS) analysis of the A. parasiticus strain SU-1 genome and comparative gene expression (RNA sequence analysis [RNA Seq]) analysis of A. parasiticus SU-1 and A. flavus strain NRRL 3357 (3357) grown under aflatoxin-inducing and -noninducing culture conditions. Although A. parasiticus SU-1 and A. flavus 3357 are highly similar in genome structure and gene organization, we observed differences in the presence of specific mycotoxin gene clusters and differential expression of specific mycotoxin genes and gene clusters that help explain differences in the type and quantity of mycotoxins synthesized. Using computer-aided analysis of secondary metabolite clusters (anti-SMASH), we demonstrated that A. parasiticus SU-1 and A. flavus 3357 may carry up to 93 secondary metabolite gene clusters, and surprisingly, up to 10% of the genome appears to be dedicated to secondary metabolite synthesis. The data also suggest that fungus-specific zinc binuclear cluster (C6) transcription factors play an important role in regulation of secondary metabolite cluster expression. Finally, we identified uniquely expressed genes in A. parasiticus SU-1 that encode C6 transcription factors and genes involved in secondary metabolism and stress response/cellular defense. Future work will focus on these differentially expressed A. parasiticus SU-1 loci to reveal their role in determining distinct species characteristics.A spergillus parasiticus and Aspergillus flavus are the predominant aflatoxin producers on susceptible crops (1). The A. flavus NRRL 3357 (3357) complete genome sequence is available (http://www.aspergillusflavus.org/genomics/), and the sequence and location of the aflatoxin biosynthetic gene cluster were determined as part of this analysis. The nucleotide sequence of the A. parasiticus SU-1 aflatoxin biosynthetic gene cluster is also available (2), and A. flavus 3357 and A. parasiticus SU-1 exhibit a high degree of sequence identity between the aflatoxin genes as well as between other genes that have been sequenced in both organisms.Although it is clear that A. flavus and A. parasiticus are closely related species, several phenotypic characteristics have been used to differentiate these species; these phenotypic characteristics include the quantity and type of mycotoxins synthesized in culture and on plants. For example, A. flavus strains synthesize predominantly B aflatoxins, while A. parasiticus strains produce both Band G-type aflatoxins (1, 3). Less than 50% of A. flavus isolates are reported to produce aflatoxins, while almost all strains of A. parasiticus are to...