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Moore GG, Mack BM, Wendt KL, Castano-Duque L, Anderson VM, Cichewicz RH. Genomic and metabolomic diversity within a familial population of Aspergillus flavus. Mol Microbiol 2024; 121:927-939. [PMID: 38396382 DOI: 10.1111/mmi.15244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/12/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024]
Abstract
Aspergillus flavus is an agriculturally significant micro-fungus having potential to contaminate food and feed crops with toxic secondary metabolites such as aflatoxin (AF) and cyclopiazonic acid (CPA). Research has shown A. flavus strains can overcome heterokaryon incompatibility and undergo meiotic recombination as teleomorphs. Although evidence of recombination in the AF gene cluster has been reported, the impacts of recombination on genotype and metabolomic phenotype in a single generation are lacking. In previous studies, we paired an aflatoxigenic MAT1-1 A. flavus strain with a non-aflatoxigenic MAT1-2 A. flavus strain that had been tagged with green fluorescent protein and then 10 F1 progenies (a mix of fluorescent and non-fluorescent) were randomly selected from single-ascospore colonies and broadly examined for evidence of recombination. In this study, we determined four of those 10 F1 progenies were recombinants because they were not vegetatively compatible with either parent or their siblings, and they exhibited other distinctive traits that could only result from meiotic recombination. The other six progenies examined shared genomic identity with the non-aflatoxigenic, fluorescent, and MAT1-2 parent, but were metabolically distinct. This study highlights phenotypic and genomic changes that may occur in a single generation from the outcrossing of sexually compatible strains of A. flavus.
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Affiliation(s)
- Geromy G Moore
- Southern Regional Research Center, USDA-ARS, New Orleans, Louisiana, USA
| | - Brian M Mack
- Southern Regional Research Center, USDA-ARS, New Orleans, Louisiana, USA
| | - Karen L Wendt
- Department of Chemistry and Biochemistry, Natural Products Discovery Group, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Lina Castano-Duque
- Southern Regional Research Center, USDA-ARS, New Orleans, Louisiana, USA
| | - Victoria M Anderson
- Department of Chemistry and Biochemistry, Natural Products Discovery Group, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Natural Products Discovery Group, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
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Molo MS, White JB, Cornish V, Gell RM, Baars O, Singh R, Carbone MA, Isakeit T, Wise KA, Woloshuk CP, Bluhm BH, Horn BW, Heiniger RW, Carbone I. Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control. PLoS One 2022; 17:e0276556. [PMID: 36301851 PMCID: PMC9620740 DOI: 10.1371/journal.pone.0276556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/08/2022] [Indexed: 11/23/2022] Open
Abstract
Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A. flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A. flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A. flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A. flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.
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Affiliation(s)
- Megan S. Molo
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - James B. White
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Vicki Cornish
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Richard M. Gell
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
- Program of Genetics, North Carolina State University, Raleigh, North
Carolina, United States of America
| | - Oliver Baars
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Rakhi Singh
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
| | - Mary Anna Carbone
- Center for Integrated Fungal Research and Department of Plant and
Microbial Biology, North Carolina State University, Raleigh, NC, United States
of America
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas AgriLife Extension
Service, Texas A&M University, College Station, TX, United States of
America
| | - Kiersten A. Wise
- Department of Plant Pathology, University of Kentucky, Princeton, KY,
United States of America
| | - Charles P. Woloshuk
- Department of Plant Pathology and Botany, Purdue University, West
Lafayette, IN, United States of America
| | - Burton H. Bluhm
- University of Arkansas Division of Agriculture, Department of Entomology
and Plant Pathology, Fayetteville, AR, United States of
America
| | - Bruce W. Horn
- United States Department of Agriculture, Agriculture Research Service,
Dawson, GA, United States of America
| | - Ron W. Heiniger
- Department of Crop and Soil Sciences, North Carolina State University,
Raleigh, NC, United States of America
| | - Ignazio Carbone
- Department of Entomology and Plant Pathology, Center for Integrated
Fungal Research, North Carolina State University, Raleigh, NC, United States of
America
- Program of Genetics, North Carolina State University, Raleigh, North
Carolina, United States of America
- * E-mail:
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Luis JM, Carbone I, Mack BM, Lebar MD, Cary JW, Gilbert MK, Bhatnagar D, Wientjes CC, Payne GA, Moore GG, Ameen YO, Ojiambo PS. Dataset for transcriptomic profiles associated with development of sexual structures in Aspergillus flavus. Data Brief 2022; 42:108033. [PMID: 35330736 PMCID: PMC8938862 DOI: 10.1016/j.dib.2022.108033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/04/2022] [Indexed: 11/17/2022] Open
Abstract
Information on the transcriptomic changes that occur within sclerotia of Aspergillus flavus during its sexual cycle is very limited and warrants further research. The findings will broaden our knowledge of the biology of A. flavus and can provide valuable insights in the development or deployment of non-toxigenic strains as biocontrol agents against aflatoxigenic strains. This article presents transcriptomic datasets included in our research article entitled, “Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus” [1], which utilized transcriptomics to identify possible genes and gene clusters associated with sexual reproduction and fertilization in A. flavus. RNA was extracted from sclerotia of a high fertility cross (Hi-Fert-Mated), a low fertility cross (Lo-Fert-Mated), and unmated strains (Hi-Fert-Unmated and Lo-Fert-Unmated) of A. flavus collected immediately after crossing and at every two weeks until eight weeks of incubation on mixed cereal agar at 30 °C in continuous darkness (n = 4 replicates from each treatment for each time point; 80 total). Raw sequencing reads obtained on an Illumina NovaSeq 6000 were deposited in NCBI's Sequence Read Archive (SRA) repository under BioProject accession number PRJNA789260. Reads were mapped to the A. flavus NRRL 3357 genome (assembly JCVI-afl1-v2.0; GCA_000006275.2) using STAR software. Differential gene expression analyses, functional analyses, and weighted gene co-expression network analysis were performed using DESeq2 R packages. The raw and analyzed data presented in this article could be reused for comparisons with other datasets to obtain transcriptional differences among strains of A. flavus or closely related species. The data can also be used for further investigation of the molecular basis of different processes involved in sexual reproduction and sclerotia fertility in A. flavus.
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