Sejal Asija
Graduate Research Assistant
University of Georgia
Athens, Georgia, United States
Ethan A. Thompson
University of Georgia
Tifton, Georgia, United States
Dongliang Wu
University of Georgia
Tifton, Georgia, United States
Sunil Gangurde
Scientist
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Hyderabad, Andhra Pradesh, India
Hamed Abbas
Research Scientist
USDA-ARS, Biological Control of Pest Research Unit
Stoneville, Mississippi, United States
Manish Pandey
International Crops Research Institute for the Semi-Arid Tropics
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Hyderabad, Andhra Pradesh, India
Jake Fountain
Assistant Professor Mycotoxicology & Postharvest Pathology
University of Georgia
Griffin, Georgia, United States
Robert C. Kemerait, Jr., PhD
Professor
UGA Dept of Plant Pathology
Tifton, GA, USA
Baozhu Guo
USDA-ARS
Tifton, Georgia, United States
Aspergillus flavus infects many important crops like corn and peanuts and producing carcinogenic aflatoxins, threatening food safety and human health. Isolates vary in genome sequences and abilities to produce aflatoxins. To capture this variation, we constructed a pangenome graph for 225 A. flavus isolates to generate a library of species variation. The graph-based pangenome identified a total of 713,035 variants, including 583,608 single nucleotide polymorphisms (SNPs) and 129,418 non-SNP variants (Indels, SV, and complex variants) with the highest variant density on chromosome 3. Phylogenetic analysis revealed two different clades, indicating distinct evolutionary lineages within the species. The aflatoxin biosynthetic cluster is present on chromosome 3, which consists of 30 genes. A genome wide association study (GWAS) with aflatoxin B1 production identified a significant location at 4.7–5.0 Mb on chromosome 3. Within the region, a 42.5 Kb deletion was identified within the aflatoxin biosynthetic cluster. Our phenotypic analysis showed that the isolates with the deletion were atoxigenic. To evaluate the completeness of this pangenome, 121 isolates were added to the graph. We found an increase of 344,367 variants to 1,057,402 (830,349 SNPs and 227,053 non-SNPs) variants, suggesting that the pangenome is non-comprehensive. The unveiling of the deletion within the biosynthetic cluster highlights the utility of a graph based pangenome in understanding the variability of A.flavus isolates to produce aflatoxin.