eprintid: 11591
rev_number: 14
eprint_status: archive
userid: 3170
dir: disk0/00/01/15/91
datestamp: 2020-09-05 09:31:14
lastmod: 2020-09-05 09:35:37
status_changed: 2020-09-05 09:31:14
type: article
metadata_visibility: show
creators_name: Fountain, J C
creators_name: Clevenger, J P
creators_name: Nadon, B
creators_name: Youngblood, R C
creators_name: Korani, W
creators_name: Chang, P K
creators_name: Starr, D
creators_name: Wang, H
creators_name: Isett, B
creators_name: Johnston, H R
creators_name: Wiggins, R
creators_name: Agarwal, G
creators_name: Chu, Y
creators_name: Kemerait, R C
creators_name: Pandey, M K
creators_name: Bhatnagar, D
creators_name: Ozias-Akins, P
creators_name: Varshney, R K
creators_name: Sheffler, B E
creators_name: Vaughn, J N
creators_name: Guo, B
icrisatcreators_name: Pandey, M K
icrisatcreators_name: Varshney, R K
affiliation: Department of Plant Pathology, University of Georgia, Tifton
affiliation: USDA-ARS, Crop Protection and Management Research Unit, Tifton
affiliation: Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkvile
affiliation: Legume Research, Mars Incorporated, Athens
affiliation: USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville
affiliation: Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Starkville
affiliation: Bioinformatics, STgenetics, Navasota
affiliation: USDA-ARS, Southern Regional Research Center, New Orleans
affiliation: Department of Plant Biology, University of Georgia, Athens
affiliation: Department of Human Genetics, Emory University, Atlanta
affiliation: Nemours Hospital for Children, Wilmington
affiliation: Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton
affiliation: ICRISAT (Patancheru)
country: USA
country: India
title: Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing To Isolate Stress Tolerance and Aflatoxin Production
ispublished: pub
subjects: s2.13
subjects: s40051
divisions: CRPS3
divisions: CRPS2
full_text_status: public
keywords: Aspergillus flavus, Aflatoxin, Reference genomes, Phylogenomics, Polyphyletic
note: 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.
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.
date: 2020-09
date_type: published
publication: G3: Genes | Genomes | Genetics (G3) (TSI)
volume: 10
number: 9
publisher: Genetics Society of America
pagerange: 1-55
id_number: doi:10.1534/g3.120.401405
refereed: TRUE
issn: 2160-1836
official_url: https://doi.org/10.1534/g3.120.401405
related_url_url: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=10.1534%2Fg3.120.401405&btnG=
related_url_type: pub
citation:   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     
document_url: http://oar.icrisat.org/11591/1/g3.120.401405.full.pdf