@article{molo_white_cornish_gell_baars_singh_carbone_isakeit_wise_woloshuk_et al._2022, title={Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control}, volume={17}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0276556}, DOI={10.1371/journal.pone.0276556}, abstractNote={Aspergillus flavusis an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B1is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenicA.flavusstrains, 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 ofA.flavusin cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815A.flavusisolates, 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 distinctA.flavusevolutionary 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.}, number={10}, journal={PLOS ONE}, author={Molo, Megan S. and White, James B. and Cornish, Vicki and Gell, Richard M. and Baars, Oliver and Singh, Rakhi and Carbone, Mary Anna and Isakeit, Thomas and Wise, Kiersten A. and Woloshuk, Charles P. and et al.}, editor={Nierman, William C.Editor}, year={2022}, month={Oct} }
 @article{moore_olarte_horn_elliott_singh_o'neal_carbone_2017, title={Global population structure and adaptive evolution of aflatoxin-producing fungi}, volume={7}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.3464}, DOI={10.1002/ece3.3464}, abstractNote={Abstract}, number={21}, journal={Ecology and Evolution}, publisher={Wiley}, author={Moore, Geromy G. and Olarte, Rodrigo A. and Horn, Bruce W. and Elliott, Jacalyn L. and Singh, Rakhi and O'Neal, Carolyn J. and Carbone, Ignazio}, year={2017}, month={Sep}, pages={9179–9191} }
 @article{horn_gell_singh_sorensen_carbone_2016, title={Sexual Reproduction in Aspergillus flavus Sclerotia: Acquisition of Novel Alleles from Soil Populations and Uniparental Mitochondrial Inheritance}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0146169}, abstractNote={Aspergillus flavus colonizes agricultural commodities worldwide and contaminates them with carcinogenic aflatoxins. The high genetic diversity of A. flavus populations is largely due to sexual reproduction characterized by the formation of ascospore-bearing ascocarps embedded within sclerotia. A. flavus is heterothallic and laboratory crosses between strains of the opposite mating type produce progeny showing genetic recombination. Sclerotia formed in crops are dispersed onto the soil surface at harvest and are predominantly produced by single strains of one mating type. Less commonly, sclerotia may be fertilized during co-infection of crops with sexually compatible strains. In this study, laboratory and field experiments were performed to examine sexual reproduction in single-strain and fertilized sclerotia following exposure of sclerotia to natural fungal populations in soil. Female and male roles and mitochondrial inheritance in A. flavus were also examined through reciprocal crosses between sclerotia and conidia. Single-strain sclerotia produced ascospores on soil and progeny showed biparental inheritance that included novel alleles originating from fertilization by native soil strains. Sclerotia fertilized in the laboratory and applied to soil before ascocarp formation also produced ascospores with evidence of recombination in progeny, but only known parental alleles were detected. In reciprocal crosses, sclerotia and conidia from both strains functioned as female and male, respectively, indicating A. flavus is hermaphroditic, although the degree of fertility depended upon the parental sources of sclerotia and conidia. All progeny showed maternal inheritance of mitochondria from the sclerotia. Compared to A. flavus populations in crops, soil populations would provide a higher likelihood of exposure of sclerotia to sexually compatible strains and a more diverse source of genetic material for outcrossing.}, number={1}, journal={PLOS ONE}, author={Horn, Bruce W. and Gell, Richard M. and Singh, Rakhi and Sorensen, Ronald B. and Carbone, Ignazio}, year={2016}, month={Jan} }
 @article{olarte_horn_singh_carbone_2015, title={Sexual recombination in Aspergillus tubingensis}, volume={107}, ISSN={["1557-2536"]}, DOI={10.3852/14-233}, abstractNote={Aspergillus tubingensis from section Nigri (black Aspergilli) is closely related to A. niger and is used extensively in the industrial production of enzymes and organic acids. We recently discovered sexual reproduction in A. tubingensis, and in this study we demonstrate that the progeny are products of meiosis. Progeny were obtained from six crosses involving five MAT1-1 strains and two MAT1-2 strains. We examined three loci, including mating type (MAT), RNA polymerase II (RPB2) and β-tubulin (BT2), and found that 84% (58/69) of progeny were recombinants. Recombination associated with sexual reproduction in A. tubingensis provides a new option for the genetic improvement of industrial strains for enzyme and organic acid production.}, number={2}, journal={MYCOLOGIA}, author={Olarte, Rodrigo A. and Horn, Bruce W. and Singh, Rakhi and Carbone, Ignazio}, year={2015}, pages={307–312} }
 @article{moore_elliott_singh_horn_dorner_stone_chulze_barros_naik_wright_et al._2013, title={Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale}, volume={9}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1003574}, DOI={10.1371/journal.ppat.1003574}, abstractNote={Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more sexual versus more asexual) is predictive of aflatoxin chemotype diversity in these agriculturally important fungi.}, number={8}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Moore, Geromy G. and Elliott, Jacalyn L. and Singh, Rakhi and Horn, Bruce W. and Dorner, Joe W. and Stone, Eric A. and Chulze, Sofia N. and Barros, German G. and Naik, Manjunath K. and Wright, Graeme C. and et al.}, editor={McDonald, Bruce A.Editor}, year={2013}, month={Aug}, pages={e1003574} }
 @article{olarte_horn_dorner_monacell_singh_stone_carbone_2012, title={Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis}, volume={21}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294x.2011.05398.x}, abstractNote={Abstract}, number={6}, journal={MOLECULAR ECOLOGY}, author={Olarte, Rodrigo A. and Horn, Bruce W. and Dorner, Joe W. and Monacell, James T. and Singh, Rakhi and Stone, Eric A. and Carbone, Ignazio}, year={2012}, month={Mar}, pages={1453–1476} }
 @article{moore_singh_horn_carbone_2009, title={Recombination and lineage-specific gene loss in the aflatoxin gene cluster of Aspergillus flavus}, volume={18}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2009.04414.x}, abstractNote={Abstract}, number={23}, journal={MOLECULAR ECOLOGY}, author={Moore, Geromy G. and Singh, Rakhi and Horn, Bruce W. and Carbone, Ignazio}, year={2009}, month={Dec}, pages={4870–4887} }