Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing To Isolate Stress Tolerance and Aflatoxin Production

    Fountain, J C and Clevenger, J P and Nadon, B and Youngblood, R C and Korani, W and Chang, P K and Starr, D and Wang, H and Isett, B and Johnston, H R and Wiggins, R and Agarwal, G and Chu, Y and Kemerait, R C and Pandey, M K and Bhatnagar, D and Ozias-Akins, P and Varshney, R K and Sheffler, B E and Vaughn, J N and Guo, B (2020) Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing To Isolate Stress Tolerance and Aflatoxin Production. G3: Genes | Genomes | Genetics (G3) (TSI), 10 (9). pp. 1-55. ISSN 2160-1836

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    Abstract

    Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae. However, less progress has been made for A. flavus. As part of the effort of the USDA ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus. Therefore, we developed two reference pseudomolecule genome assemblies derived from chromosome arms for two isolates: AF13, a MAT1-2, highly stress tolerant, and highly aflatoxigenic isolate; and NRRL3357, a MAT1-1, less stress tolerant, and moderate aflatoxin producer in comparison to AF13. Here, we report these two reference grade assemblies for these isolates through a combination of PacBio long-read sequencing and optical mapping, and coupled them with comparative, functional, and phylogenetic analyses. This analysis resulted in the identification of 153 and 45 unique genes in AF13 and NRRL3357, respectively. We also confirmed the presence of a unique 310 Kb insertion in AF13 containing 58 genes. Analysis of this insertion revealed the presence of a bZIP transcription factor, named atfC, which may contribute to isolate pathogenicity and stress tolerance. Phylogenomic analyses comparing these and other available assemblies also suggest that the species complex of A. flavus is polyphyletic.

    Item Type: Article
    Divisions: Research Program : Genetic Gains
    Research Program : Asia
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Aspergillus flavus, Aflatoxin, Reference genomes, Phylogenomics, Polyphyletic
    Subjects: Others > Genetics and Genomics
    Others > Aflatoxins
    Depositing User: Mr Arun S
    Date Deposited: 05 Sep 2020 09:31
    Last Modified: 05 Sep 2020 09:35
    URI: http://oar.icrisat.org/id/eprint/11591
    Official URL: https://doi.org/10.1534/g3.120.401405
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: We would like to thank Billy Wilson, Sheron Simpson, and Leslie Scharfenstein for technical assistance in the laboratory. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The USDA is an equal opportunity employer and provider.
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