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

Autor: Fountain JC; Department of Plant Pathology, University of Georgia, Tifton, GA 31793.; USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA 31793.; Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762., Clevenger JP; Legume Research, Mars Incorporated, Athens, GA 30605., Nadon B; USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS 38776., Youngblood RC; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Starkville, MS 39762., Korani W; Bioinformatics, STgenetics, Navasota, TX 77868., Chang PK; USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124., Starr D; Department of Plant Biology, University of Georgia, Athens, GA 30605., Wang H; Department of Plant Pathology, University of Georgia, Tifton, GA 31793.; USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA 31793., Isett B; Department of Human Genetics, Emory University, Atlanta, GA 30322.; Nemours Hospital for Children, Wilmington, DE 19803., Johnston HR; Department of Human Genetics, Emory University, Atlanta, GA 30322., Wiggins R; Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793., Agarwal G; Department of Plant Pathology, University of Georgia, Tifton, GA 31793., Chu Y; Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793., Kemerait RC; Department of Plant Pathology, University of Georgia, Tifton, GA 31793., Pandey MK; International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana 502324, India., Bhatnagar D; USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124., Ozias-Akins P; Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA 31793., Varshney RK; International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana 502324, India., Scheffler BE; USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS 38776 baozhu.guo@usda.gov justin.vaughn@usda.gov brian.scheffler@usda.gov., Vaughn JN; USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS 38776 baozhu.guo@usda.gov justin.vaughn@usda.gov brian.scheffler@usda.gov., Guo B; USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA 31793 baozhu.guo@usda.gov justin.vaughn@usda.gov brian.scheffler@usda.gov.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2020 Oct 05; Vol. 10 (10), pp. 3515-3531. Date of Electronic Publication: 2020 Oct 05.
DOI: 10.1534/g3.120.401405
Abstrakt: 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.
(Copyright © 2020 Fountain et al.)
Databáze: MEDLINE
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