Table S1 Predicted genes on the right arm of chromosome 3 of Aspergillus flavus.

Table S2 Distribution of haplotypes and base substitutions in the aflG/aflL intergenic region of 63 natural Aspergillus flavus isolates, including AF36, plus progeny isolate IC1716.

Table S3 Haplotypes and strain designations for the aflG/aflL intergenic region haplotype distribution map shown in Table S2 (Supporting information).

Table S4 Distribution of haplotypes, base substitutions, and insertion/deletion events in LD plot and site compatibility matrix shown in Fig. 4.

Table S5 Haplotypes and strain designations in Table S4 (Supporting information).

Table S6 Distribution of haplotypes, base substitutions, and insertion/deletion events in the ARG shown in Fig. 5.

Table S7 Haplotypes and strain designations for the Aspergillus flavus ARG in Fig. 5.

Table S8 Haplotypes and strain designations in Fig. 6.

Fig. S1. Genome-wide parentage plots for the parent-offspring trio heat maps shown in Figures 2 and 3. Each of the plots labeled from A-I corresponds to one offspring. In the plots, a black vertical line indicates the centromere, and blue vertical lines indicate the locations of the loci used in our multilocus sequence typing (MLST). Microsatellite locus AF17 is represented on chromosome 2; AF cluster loci aflC, aflG/aflL, aflV/aflW, aflW/aflX and linked locus mfs are on chromosome 3; the trpC locus is on chromosome 4; and the mating-type locus (MAT) is on chromosome 6. Each red dot in the chromosome plot identifies one probe. On the x-axis is the approximate position of the probe on the chromosome in Mb; on the y-axis is the degree of similarity of the offspring to each parent, which is a score that predicts parental origin. Chromosomes showing different parental origins along their entire length in the progeny would be indicative of independent assortment. For example, in Figure S1A, a negative difference for most of the probes on chromosome 8 suggests that progeny strain IC1650 is more similar to AF36, which is the bottom parent in the plot, whereas a positive difference for the probes in chromosome 5 translates to IC1650 showing more similarity to IC278, the top parent in the plot. Alternating probe patterns indicate that a crossover has occurred. For example, at least one crossover can be discerned in the rightmost portion of chromosome 3R, which is corroborated with our genetic markers in the AF cluster.

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