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

• Type of Material: Article
• Authors: Jake C. Fountain, University of Georgia; Josh P. Clevenger, Mars Incorporated; Brian Nadon, USDA ARS; Ramey C. Youngblood, Mississippi State University; Walid Korani, STgenetics; Perng-Kuang Chang, USDA ARS; Dakota Starr, University of Georgia; Hui Wang, Emory University; Benjamin Isett, Emory University; H. Richard Johnston, Emory University; Raegan Wiggins, University of Georgia; Gaurav Agarwal, University of Georgia; Ye Chu, University of Georgia; Robert C. Kemerait, University of Georgia; Manish K. Pandey, International Crop Research Institute for the Semi-Arid Tropics; Deepak Bhatnagar, USDA ARS; Peggy Ozias-Akins, University of Georgia; Rajeev K. Varshney, International Crop Research Institute for the Semi-Arid Tropics; Brian E. Scheffler, USDA ARS; Justin N. Vaughn, USDA ARS; Baozhu Guo, USDA ARS
• Language: English
• Date: 2020-10-01
• Publisher: GENETICS SOCIETY AMERICA
• Publication Version: Final Published Version
• Copyright Statement: © 2020 Fountain et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1534/g3.120.401405
• Title of Journal or Parent Work: G3-GENES GENOMES GENETICS
• Volume: 10
• Issue: 10
• Start Page: 3515
• End Page: 3531
• Keywords: phylogenomics; aflatoxin; polyphyletic; RELATEDNESS; Life Sciences & Biomedicine; reference genomes; Science & Technology; IDENTIFICATION; ASPERGILLUS-FLAVUS; OXIDATIVE STRESS; GENE-CLUSTER; BIOSYNTHESIS CLUSTER; Aspergillus flavus; SEQUENCE; Genetics & Heredity; RESISTANCE; RECOMBINATION; TRANSFORMATION
• Research Categories: Biology, Genetics; Health Sciences, Pathology

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 60 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.