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

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Relation http://oar.icrisat.org/12657/
https://link.springer.com/article/10.1186/s12870-024-04950-8
https://doi.org/10.1186/s12870-024-04950-8
 
Title Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters
 
Creator Gangurde, S S
Korani, W
Bajaj, P
Wang, H
Fountain, J C
Agarwal, G
Pandey, M K
Abbas, H K
Chang, P K
Holbrook, C C
Kemerait, R C
Varshney, R K
Dutta, B
Clevenger, J P
Guo, B
 
Subject Genetics and Genomics
Aflatoxins
 
Description Background
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. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.

Results
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.

Conclusion
In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.
 
Publisher BioMed Central
 
Date 2024-05-01
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12657/1/BMC%20Plant%20Biology_24_1-17_2024.pdf
Gangurde, S S and Korani, W and Bajaj, P and Wang, H and Fountain, J C and Agarwal, G and Pandey, M K and Abbas, H K and Chang, P K and Holbrook, C C and Kemerait, R C and Varshney, R K and Dutta, B and Clevenger, J P and Guo, B (2024) Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters. BMC Plant Biology (TSI), 24. pp. 1-17. ISSN 1471-2229