Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters

Authors: GANGURDE, SUNIL - University Of Georgia; KORANI, WALID - Hudsonalpha Institute For Biotechnology; BAJAJ, PRASAD - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; WANG, HUI - University Of Georgia; FOUNTAIN, JAKE - University Of Georgia; AGARWAL, GAURAV - Michigan State University; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Abbas, Hamed; Chang, Perng Kuang; Holbrook, Carl - Corley; KEMERAIT, ROBERT - University Of Georgia; VARSHNEY, RAJEEV - Murdoch University; DUTTA, BHABESH - University Of Georgia; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology; Guo, Baozhu

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2024
Publication Date: 5/1/2024
Citation: Gangurde, S., Korani, W., Bajaj, P., Wang, H., Fountain, J.C., Agarwal, G., Pandey, M.K., Abbas, H.K., Chang, P., Holbrook Jr, C.C., Kemerait, R.C., Varshney, R.K., Dutta, B., Pandey, M.K., Clevenger, J.P., Guo, B. 2024. Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters. BMC Plant Biology. 24:354. https://doi.org/10.1186/s12870-024-04950-8.
DOI: https://doi.org/10.1186/s12870-024-04950-8

Interpretive Summary: Aspergillus flavus is an opportunistic saprophyte, infects varieties of crops such as corn and peanuts both pre- and postharvest. These fungi also produce secondary metabolites including aflatoxins which contaminate the grains and are toxic and carcinogenic. Therefore, a pan-genomic approach is necessary to fully capture the genetic diversity present in the A. flavus species, particularly in agricultural environments, and can be used to perform in depth studies of secondary metabolite gene clusters and their regulation. To accomplish this, present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources; (2) whole genome sequencing of collected isolates and development of a pan-genome; and (3) to conduct pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite genes. This A. flavus pangenome, named AflaPan, can serve as a new reference for comparative genomics studies by research community.

Technical Abstract: Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Here, pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites. Furthermore, 256 novel pan-genes associated with potential aflatoxin production were not annotated in current reference genomes of A. flavus. Therefore, this A. flavus pangenome is a closed pangenome and represents a large number of genes unreported in previous single reference genome assemblies.