@article{jana m. u'ren_oita_lutzoni_miadlikowska_ball_carbone_may_zimmerman_valle_trouet_et al._2024, title={Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth's largest terrestrial biome}, volume={34}, ISSN={["1879-0445"]}, DOI={10.1016/j.cub.2024.01.063}, abstractNote={<h2>Summary</h2> Understanding how symbiotic associations differ across environmental gradients is key to predicting the fate of symbioses as environments change, and it is vital for detecting global reservoirs of symbiont biodiversity in a changing world.<sup>1</sup><sup>,</sup><sup>2</sup><sup>,</sup><sup>3</sup> However, sampling of symbiotic partners at the full-biome scale is difficult and rare. As Earth's largest terrestrial biome, boreal forests influence carbon dynamics and climate regulation at a planetary scale. Plants and lichens in this biome host the highest known phylogenetic diversity of fungal endophytes, which occur within healthy photosynthetic tissues and can influence hosts' resilience to stress.<sup>4</sup><sup>,</sup><sup>5</sup> We examined how communities of endophytes are structured across the climate gradient of the boreal biome, focusing on the dominant plant and lichen species occurring across the entire south-to-north span of the boreal zone in eastern North America. Although often invoked for understanding the distribution of biodiversity, neither a latitudinal gradient nor mid-domain effect<sup>5</sup><sup>,</sup><sup>6</sup><sup>,</sup><sup>7</sup> can explain variation in endophyte diversity at this trans-biome scale. Instead, analyses considering shifts in forest characteristics, <i>Picea</i> biomass and age, and nutrients in host tissues from 46° to 58° N reveal strong and distinctive signatures of climate in defining endophyte assemblages in each host lineage. Host breadth of endophytes varies with climate factors, and biodiversity hotspots can be identified at plant-community transitions across the boreal zone at a global scale. Placed against a backdrop of global circumboreal sampling,<sup>4</sup> our study reveals the sensitivity of endophytic fungi, their reservoirs of biodiversity, and their important symbiotic associations, to climate.}, number={5}, journal={CURRENT BIOLOGY}, author={Jana M. U'Ren and Oita, Shuzo and Lutzoni, Francois and Miadlikowska, Jolanta and Ball, Bernard and Carbone, Ignazio and May, Georgiana and Zimmerman, Naupaka B. and Valle, Denis and Trouet, Valerie and et al.}, year={2024}, month={Mar} }
 @article{coomber_saville_carbone_ristaino_2023, title={An open-access T-BAS phylogeny for emerging Phytophthora species}, volume={18}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0283540}, DOI={10.1371/journal.pone.0283540}, abstractNote={Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.}, number={4}, journal={PLOS ONE}, author={Coomber, Allison and Saville, Amanda and Carbone, Ignazio and Ristaino, Jean Beagle}, editor={Blair, Jaime E.Editor}, year={2023}, month={Apr} }
 @article{hoz_magain_piatkowski_cornet_dal forno_carbone_miadlikowska_lutzoni_2023, title={Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria}, volume={2}, ISSN={["1076-836X"]}, url={https://doi.org/10.1093/sysbio/syad008}, DOI={10.1093/sysbio/syad008}, abstractNote={Abstract}, journal={SYSTEMATIC BIOLOGY}, author={Hoz, Carlos J. and Magain, Nicolas and Piatkowski, Bryan and Cornet, Luc and Dal Forno, Manuela and Carbone, Ignazio and Miadlikowska, Jolanta and Lutzoni, Francois}, editor={Lemus-Solis, ClaudiaEditor}, year={2023}, month={Feb} }
 @article{dye_muga_mwangi_hoyer_ly_rosado_sharpee_mware_wambugu_labadie_et al._2023, title={Cassava begomovirus species diversity changes during plant vegetative cycles}, volume={14}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2023.1163566}, DOI={10.3389/fmicb.2023.1163566}, abstractNote={Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Dye, Anna E. and Muga, Brenda and Mwangi, Jenniffer and Hoyer, J. Steen and Ly, Vanessa and Rosado, Yamilex and Sharpee, William and Mware, Benard and Wambugu, Mary and Labadie, Paul and et al.}, year={2023}, month={May} }
 @article{miadlikowska_magain_medeiros_hoz_carbone_lagreca_barlow_myllys_schmull_lutzoni_2023, title={Towards a nomenclatural clarification of the <i>Peltigera ponojensis/monticola</i> clade including metagenomic sequencing of type material and the introduction of <i>P. globulata</i> Miadl. & Magain sp. nov.}, volume={55}, ISSN={["1096-1135"]}, url={https://doi.org/10.1017/S0024282923000373}, DOI={10.1017/S0024282923000373}, abstractNote={Abstract}, number={5}, journal={LICHENOLOGIST}, author={Miadlikowska, Jolanta and Magain, Nicolas and Medeiros, Ian D. and Hoz, Carlos J. and Carbone, Ignazio and LaGreca, Scott and Barlow, Thomas and Myllys, Leena and Schmull, Michaela and Lutzoni, Francois}, year={2023}, month={Sep}, pages={315–324} }
 @article{jin_mccorkle_cornish_carbone_lewis_shew_2022, title={Adaptation of Phytophthora nicotianae to Multiple Sources of Partial Resistance in Tobacco}, volume={106}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-06-21-1241-RE}, abstractNote={ Host resistance is an important tool in the management of black shank disease of tobacco. Race development leads to rapid loss of single-gene resistance, but the adaptation by Phytophthora nicotianae to sources of partial resistance from Beinhart 1000, Florida 301, and the Wz gene region introgressed from Nicotiana rustica is poorly characterized. In greenhouse environments, host genotypes with quantitative trait loci (QTLs) conferring resistance from multiple sources were initially inoculated with an aggressive isolate of race 0 or race 1 of P. nicotianae. The most aggressive isolate was selected after each of six host generations to inoculate the next generation of plants. The race 0 isolate demonstrated a continuous gradual increase in disease severity and percentage root rot on all sources of resistance except the genotype K 326 Wz/–, where a large increase in both was observed between generations 2 and 3. Adaptation by the race 0 isolate on Beinhart 1000 represents the first report of adaptation to this genotype by P. nicotianae. The race 1 isolate did not exhibit significant increases in aggressiveness over generations but exhibited a large increase in aggressiveness on K 326 Wz/– between generations 3 and 4. Molecular characterization of isolates recovered during selection was completed via double digest restriction-site associated DNA sequencing, but no polymorphisms were associated with the observed changes in aggressiveness. The rapid adaptation to Wz resistance and the gradual adaptation to other QTLs highlights the need to study the nature of Wz resistance and to conduct field studies on the efficacy of resistance gene rotation for disease management. }, number={3}, journal={PLANT DISEASE}, author={Jin, Jing and McCorkle, Kestrel L. and Cornish, Vicki and Carbone, Ignazio and Lewis, Ramsey S. and Shew, H. David}, year={2022}, month={Mar}, pages={906–917} }
 @article{aimone_hoyer_dye_deppong_duffy_carbone_hanley-bowdoin_2022, title={An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing}, volume={300}, ISSN={["1879-0984"]}, url={http://dx.doi.org/10.1016/j.jviromet.2021.114405}, DOI={10.1016/j.jviromet.2021.114405}, abstractNote={The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.}, journal={JOURNAL OF VIROLOGICAL METHODS}, publisher={Elsevier BV}, author={Aimone, Catherine D. and Hoyer, J. Steen and Dye, Anna E. and Deppong, David O. and Duffy, Siobain and Carbone, Ignazio and Hanley-Bowdoin, Linda}, year={2022}, month={Feb} }
 @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{luis_carbone_mack_lebar_cary_gilbert_bhatnagar_wientjes_payne_moore_et al._2022, title={Dataset for transcriptomic profiles associated with development of sexual structures in Aspergillus flavus}, volume={42}, ISSN={["2352-3409"]}, DOI={10.1016/j.dib.2022.108033}, abstractNote={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.}, journal={DATA IN BRIEF}, author={Luis, Jane Marian and Carbone, Ignazio and Mack, Brian M. and Lebar, Matthew D. and Cary, Jeffrey W. and Gilbert, Matthew K. and Bhatnagar, Deepak and Wientjes, Carol-Carter and Payne, Gary A. and Moore, Geromy G. and et al.}, year={2022}, month={Jun} }
 @article{luis_carbone_mack_lebar_cary_gilbert_bhatnagar_wientjes_payne_moore_et al._2022, title={Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus}, volume={126}, ISSN={["1878-6162"]}, DOI={10.1016/j.funbio.2022.01.001}, abstractNote={Sclerotium (female) fertility, the ability of a strain to produce ascocarps, influences internal morphological changes during sexual reproduction in Aspergillus flavus. Although sclerotial morphogenesis has been linked to secondary metabolite (SM) biosynthesis, metabolic and transcriptomic changes within A. flavus sclerotia during sexual development are not known. Successful mating between compatible strains may result in relatively high or low numbers of ascocarps being produced. Sclerotia from a high fertility cross (Hi-Fert-Mated), a low fertility cross (Lo-Fert-Mated), unmated strains (Hi-Fert-Unmated and Lo-Fert-Unmated) were harvested immediately after crosses were made and every two weeks until 8 weeks of incubation, then subjected to targeted metabolomics (n = 106) and transcriptomics analyses (n = 80). Aflatoxin B1 production varied between Hi-Fert-Mated and Hi-Fert-Unmated sclerotia, while it remained low or was undetected in Lo-Fert-Mated and Lo-Fert-Unmated sclerotia. Profiling of 14 SMs showed elevated production of an aflavazole analog, an aflavinine isomer, and hydroxyaflavinine in Hi-Fert-Mated sclerotia at 4 to 8 weeks. Similarly, genes ayg1, hxtA, MAT1, asd-3, preA and preB, and genes in uncharacterized SM gene clusters 30 and 44 showed increased expression in Hi-Fert-Mated sclerotia at these time points. These results broaden our knowledge of the biochemical and transcriptional processes during sexual development in A. flavus.}, number={3}, journal={FUNGAL BIOLOGY}, author={Luis, Jane Marian and Carbone, Ignazio and Mack, Brian M. and Lebar, Matthew D. and Cary, Jeffrey W. and Gilbert, Matthew K. and Bhatnagar, Deepak and Wientjes, Carol-Carter and Payne, Gary A. and Moore, Geromy G. and et al.}, year={2022}, month={Mar}, pages={187–200} }
 @article{hu_govers_carbone_ristaino_2022, title={Gene Flow of Phytophthora infestans Between Refuse Piles, and Organic and Conventional Potato Fields in Southern Flevoland, The Netherlands}, volume={11}, ISSN={["1871-4528"]}, url={https://doi.org/10.1007/s11540-022-09597-2}, DOI={10.1007/s11540-022-09597-2}, journal={POTATO RESEARCH}, author={Hu, Chia-Hui and Govers, Francine and Carbone, Ignazio and Ristaino, Jean Beagle}, year={2022}, month={Nov} }
 @article{ahmad_zervas_ellegaard-jensen_hennessy_carbone_cornish_muller-stover_grunden_jacobsen_nicolaisen_2022, title={Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage}, volume={10}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00663-22}, abstractNote={Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four wheat cultivars grown under controlled conditions and sampled after flag leaf emergence are provided. Data demonstrate differences in microbial communities according to rhizocompartment.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Ahmad, Jabeen and Zervas, Athanasios and Ellegaard-Jensen, Lea and Hennessy, Rosanna C. and Carbone, Ignazio and Cornish, Vicki and Muller-Stover, Dorette Sophie and Grunden, Amy and Jacobsen, Carsten S. and Nicolaisen, Mette Haubjerg}, year={2022}, month={Oct} }
 @article{hoyer_wilkins_munshi_wiese_dubey_renard_mortensen_dye_carbone_duffy_et al._2022, title={Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana}, volume={6}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-12-21-0077-R}, abstractNote={ Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the replication-associated ( Rep) gene were readily compensated for by direct reversion or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B), indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Columbia-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks. }, number={3}, journal={PHYTOBIOMES JOURNAL}, author={Hoyer, J. Steen and Wilkins, Olivia W. and Munshi, Aanandi and Wiese, Emma and Dubey, Divya and Renard, Savannah and Mortensen, Karoline Rosendal Harto and Dye, Anna E. and Carbone, Ignazio and Duffy, Siobain and et al.}, year={2022}, pages={227–235} }
 @article{guo_carbone_rasmussen_2022, title={Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination}, volume={18}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1010422}, abstractNote={Movement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungusAspergillus flavussampled across the United States to explore patterns of recombination and migration across the genome.}, number={8}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Guo, Fangfang and Carbone, Ignazio and Rasmussen, David A.}, year={2022}, month={Aug} }
 @article{oita_ibanez_lutzoni_miadlikowska_geml_lewis_hom_carbone_jana m. u'ren_arnold_2021, title={Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale}, volume={4}, ISSN={["2399-3642"]}, DOI={10.1038/s42003-021-01826-7}, abstractNote={Abstract}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Oita, Shuzo and Ibanez, Alicia and Lutzoni, Francois and Miadlikowska, Jolanta and Geml, Jozsef and Lewis, Louise A. and Hom, Erik F. Y. and Carbone, Ignazio and Jana M. U'Ren and Arnold, A. Elizabeth}, year={2021}, month={Mar} }
 @article{crouch_beirn_boehm_carbone_clarke_kerns_malapi-wight_mitchell_venu_tredway_2021, title={Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana}, volume={105}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-06-20-1296-A}, abstractNote={ Fungi in the genus Clarireedia are widespread and destructive pathogens of grasses worldwide, and are best known as the causal agents of dollar spot disease in turfgrass. Here, we report genome assemblies of seven Clarireedia isolates, including ex-types of the two most widespread species, Clarireedia jacksonii and C. monteithiana. These datasets provide a valuable resource for ongoing studies of the dollar spot pathogens that include population diversity, host–pathogen interactions, marker development, and disease control. }, number={3}, journal={PLANT DISEASE}, author={Crouch, Jo Anne and Beirn, Lisa A. and Boehm, Michael J. and Carbone, Ignazio and Clarke, Bruce B. and Kerns, James P. and Malapi-Wight, Martha and Mitchell, Thomas K. and Venu, R. C. and Tredway, Lane P.}, year={2021}, month={Mar}, pages={691–694} }
 @article{oita_carey_kline_ibanez_yang_hom_carbone_jana m. u'ren_arnold_2021, title={Methodological Approaches Frame Insights into Endophyte Richness and Community Composition}, volume={82}, ISSN={["1432-184X"]}, DOI={10.1007/s00248-020-01654-y}, abstractNote={Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.}, number={1}, journal={MICROBIAL ECOLOGY}, author={Oita, Shuzo and Carey, Jamison and Kline, Ian and Ibanez, Alicia and Yang, Nathaniel and Hom, Erik F. Y. and Carbone, Ignazio and Jana M. U'Ren and Arnold, A. Elizabeth}, year={2021}, month={Jul}, pages={21–34} }
 @article{kayleigh r. o'keeffe_halliday_jones_carbone_mitchell_2021, title={Parasites, niche modification and the host microbiome: A field survey of multiple parasites}, volume={30}, ISSN={["1365-294X"]}, DOI={10.1111/mec.15892}, abstractNote={Abstract}, number={10}, journal={MOLECULAR ECOLOGY}, author={Kayleigh R. O'Keeffe and Halliday, Fletcher W. and Jones, Corbin D. and Carbone, Ignazio and Mitchell, Charles E.}, year={2021}, month={May}, pages={2404–2416} }
 @article{aimone_lavington_hoyer_deppong_mickelson-young_jacobson_kennedy_carbone_hanley-bowdoin_duffy_2021, title={Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation}, volume={102}, ISSN={0022-1317 1465-2099}, url={http://dx.doi.org/10.1099/jgv.0.001622}, DOI={10.1099/jgv.0.001622}, abstractNote={Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5′ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.}, number={7}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Aimone, Catherine D. and Lavington, Erik and Hoyer, J. Steen and Deppong, David O. and Mickelson-Young, Leigh and Jacobson, Alana and Kennedy, George G. and Carbone, Ignazio and Hanley-Bowdoin, Linda and Duffy, Siobain}, year={2021}, month={Jul} }
 @article{luis_carbone_payne_bhatnagar_cary_moore_lebar_wei_mack_ojiambo_2020, title={Characterization of morphological changes within stromata during sexual reproduction inAspergillus flavus}, volume={112}, ISSN={["1557-2536"]}, DOI={10.1080/00275514.2020.1800361}, abstractNote={ABSTRACT Aspergillus flavus contaminates agricultural products worldwide with carcinogenic aflatoxins that pose a serious health risk to humans and animals. The fungus survives adverse environmental conditions through production of sclerotia. When fertilized by a compatible conidium of an opposite mating type, a sclerotium transforms into a stroma within which ascocarps, asci, and ascospores are formed. However, the transition from a sclerotium to a stroma during sexual reproduction in A. flavus is not well understood. Early events during the interaction between sexually compatible strains of A. flavus were visualized using conidia of a green fluorescent protein (GFP)-labeled MAT1-1 strain and sclerotia of an mCherry-labeled MAT1-2 strain. Both conidia and sclerotia of transformed strains germinated to produce hyphae within 24 h of incubation. Hyphal growth of these two strains produced what appeared to be a network of interlocking hyphal strands that were observed at the base of the mCherry-labeled sclerotia (i.e., region in contact with agar surface) after 72 h of incubation. At 5 wk following incubation, intracellular green-fluorescent hyphal strands were observed within the stromatal matrix of the mCherry-labeled strain. Scanning electron microscopy of stromata from a high- and low-fertility cross and unmated sclerotia was used to visualize the formation and development of sexual structures within the stromatal and sclerotial matrices, starting at the time of crossing and thereafter every 2 wk until 8 wk of incubation. Morphological differences between sclerotia and stromata became apparent at 4 wk of incubation. Internal hyphae and croziers were detected inside multiple ascocarps that developed within the stromatal matrix of the high-fertility cross but were not detected in the matrix of the low-fertility cross or the unmated sclerotia. At 6 to 8 wk of incubation, hyphal tips produced numerous asci, each containing one to eight ascospores that emerged out of an ascus following the breakdown of the ascus wall. These observations broaden our knowledge of early events during sexual reproduction and suggest that hyphae from the conidium-producing strain may be involved in the early stages of sexual reproduction in A. flavus. When combined with omics data, these findings could be useful in further exploration of the molecular and biochemical mechanisms underlying sexual reproduction in A. flavus.}, number={5}, journal={MYCOLOGIA}, author={Luis, Jane Marian and Carbone, Ignazio and Payne, Gary A. and Bhatnagar, Deepak and Cary, Jeffrey W. and Moore, Geromy G. and Lebar, Matthew D. and Wei, Qijian and Mack, Brian and Ojiambo, Peter S.}, year={2020}, month={Sep}, pages={908–920} }
 @article{molo_heiniger_boerema_carbone_2019, title={A Response to the Letter to the Editor from Ortega-Beltran and Bandyopadhyay}, volume={111}, number={5}, journal={Agronomy Journal}, author={Molo, M. and Heiniger, R. and Boerema, L. and Carbone, I.}, year={2019}, month={Sep}, pages={2629–2631} }
 @article{lewis_carbone_luis_payne_bowen_hagan_kemerait_heiniger_ojiambo_2019, title={Biocontrol Strains Differentially Shift the Genetic Structure of Indigenous Soil Populations of Aspergillus flavus}, volume={10}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2019.01738}, DOI={10.3389/fmicb.2019.01738}, abstractNote={Biocontrol using non-aflatoxigenic strains of Aspergillus flavus has the greatest potential to mitigate aflatoxin contamination in agricultural produce. However, factors that influence the efficacy of biocontrol agents in reducing aflatoxin accumulation under field conditions are not well-understood. Shifts in the genetic structure of indigenous soil populations of A. flavus following application of biocontrol products Afla-Guard and AF36 were investigated to determine how these changes can influence the efficacy of biocontrol strains in reducing aflatoxin contamination. Soil samples were collected from maize fields in Alabama, Georgia, and North Carolina in 2012 and 2013 to determine changes in the population genetic structure of A. flavus in the soil following application of the biocontrol strains. A. flavus L was the most dominant species of Aspergillus section Flavi with a frequency ranging from 61 to 100%, followed by Aspergillus parasiticus that had a frequency of <35%. The frequency of A. flavus L increased, while that of A. parasiticus decreased after application of biocontrol strains. A total of 112 multilocus haplotypes (MLHs) were inferred from 1,282 isolates of A. flavus L using multilocus sequence typing of the trpC, mfs, and AF17 loci. A. flavus individuals belonging to the Afla-Guard MLH in the IB lineage were the most dominant before and after application of biocontrol strains, while individuals of the AF36 MLH in the IC lineage were either recovered in very low frequencies or not recovered at harvest. There were no significant (P > 0.05) differences in the frequency of individuals with MAT1-1 and MAT1-2 for clone-corrected MLH data, an indication of a recombining population resulting from sexual reproduction. Population mean mutation rates were not different across temporal and spatial scales indicating that mutation alone is not a driving force in observed multilocus sequence diversity. Clustering based on principal component analysis identified two distinct evolutionary lineages (IB and IC) across all three states. Additionally, patristic distance analysis revealed phylogenetic incongruency among single locus phylogenies which suggests ongoing genetic exchange and recombination. Levels of aflatoxin accumulation were very low except in North Carolina in 2012, where aflatoxin levels were significantly (P < 0.05) lower in grain from treated compared to untreated plots. Phylogenetic analysis showed that Afla-Guard was more effective than AF36 in shifting the indigenous soil populations of A. flavus toward the non-toxigenic or low aflatoxin producing IB lineage. These results suggest that Afla-Guard, which matches the genetic and ecological structure of indigenous soil populations of A. flavus in Alabama, Georgia, and North Carolina, is likely to be more effective in reducing aflatoxin accumulation and will also persist longer in the soil than AF36 in the southeastern United States.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Lewis, Mary H. and Carbone, Ignazio and Luis, Jane M. and Payne, Gary A. and Bowen, Kira L. and Hagan, Austin K. and Kemerait, Robert and Heiniger, Ron and Ojiambo, Peter S.}, year={2019}, month={Jul} }
 @article{gell_carbone_2019, title={HPLC quantitation of aflatoxin B1 from fungal mycelium culture}, volume={158}, ISSN={0167-7012}, url={http://dx.doi.org/10.1016/j.mimet.2019.01.008}, DOI={10.1016/j.mimet.2019.01.008}, abstractNote={Aflatoxins are mycotoxins that contaminate agricultural products when infected by toxigenic Aspergillus flavus. Methods for quantifying aflatoxin from culture using chromatography are available but are not optimized for population studies. We provide details of a method for preparation and quantitation of aflatoxin B1 from fungal cultures that satisfy those needs.}, journal={Journal of Microbiological Methods}, publisher={Elsevier BV}, author={Gell, Richard M. and Carbone, Ignazio}, year={2019}, month={Mar}, pages={14–17} }
 @article{u’ren_lutzoni_miadlikowska_zimmerman_carbone_may_arnold_2019, title={Host availability drives distributions of fungal endophytes in the imperilled boreal realm}, volume={3}, ISSN={2397-334X}, url={http://dx.doi.org/10.1038/s41559-019-0975-2}, DOI={10.1038/s41559-019-0975-2}, abstractNote={Boreal forests represent the world's largest terrestrial biome and provide ecosystem services of global importance. Highly imperilled by climate change, these forests host Earth's greatest phylogenetic diversity of endophytes, a hyperdiverse group of symbionts that are defined by their occurrence within living, symptomless plant and lichen tissues. Endophytes shape the ecological and evolutionary trajectories of plants and are therefore key to the function and resilience of terrestrial ecosystems. A critical step in linking the ecological functions of endophytes with those of their hosts is to understand the distributions of these symbionts at the global scale; however, turnover in host taxa with geography and climate can confound insights into endophyte biogeography. As a result, global drivers of endophyte diversity and distributions are not known. Here, we leverage sampling from phylogenetically diverse boreal plants and lichens across North America and Eurasia to show that host filtering in distinctive environments, rather than turnover with geographical or environmental distance, is the main determinant of the community composition and diversity of endophytes. We reveal the distinctiveness of boreal endophytes relative to soil fungi worldwide and endophytes from diverse temperate biomes, highlighting a high degree of global endemism. Overall, the distributions of endophytes are directly linked to the availability of compatible hosts, highlighting the role of biotic interactions in shaping fungal communities across large spatial scales, and the threat that climate change poses to biological diversity and function in the imperilled boreal realm.}, number={10}, journal={Nature Ecology & Evolution}, publisher={Springer Science and Business Media LLC}, author={U’Ren, Jana M. and Lutzoni, François and Miadlikowska, Jolanta and Zimmerman, Naupaka B. and Carbone, Ignazio and May, Georgiana and Arnold, A. Elizabeth}, year={2019}, month={Sep}, pages={1430–1437} }
 @article{koehler_larkin_rogers_carbone_cubeta_shew_2019, title={Identification and characterization of Septoria steviae as the causal agent of Septoria leaf spot disease of stevia in North Carolina}, volume={111}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.1080/00275514.2019.1584503}, DOI={10.1080/00275514.2019.1584503}, abstractNote={ABSTRACT Stevia (Stevia rebaudiana) is an emerging perennial crop in the southeastern United States. A Septoria leaf spot disease of stevia was first identified on field plantings in Japan in 1978. The pathogen was named Septoria steviae based on a morphological characterization. In 2015, a species of Septoria with morphological characters of S. steviae was isolated from field and greenhouse-grown stevia plants with leaf spot symptoms in North Carolina. In this study, 12 isolates obtained from diseased stevia plants in 2015 and 2016 were characterized and compared with reference strains of S. steviae. Comparisons were based on conidial and pycnidial morphology and multilocus sequence analysis of actin (ACT), β-tubulin (BT), calmodulin (CAL), nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2 = ITS), nuc rDNA 28S subunit (28S), RNA polymerase II second largest subunit (RPB2), and translation elongation factor-1α (TEF1). Measurements of conidia and pycnidia from symptomatic field leaves and 12 pure cultures grown on nutrient medium were consistent with those previously reported for ex-type strains of S. steviae. North Carolina strains formed a well-supported monophyletic group with ex-type strains of S. steviae. This study represents the first genetic characterization of S. steviae in the United States and provides an experimental framework to elucidate the genetic diversity and disease ecology of field populations of S. steviae.}, number={3}, journal={Mycologia}, publisher={Informa UK Limited}, author={Koehler, Alyssa M. and Larkin, Maximo T. and Rogers, Layne W. and Carbone, Ignazio and Cubeta, Marc A. and Shew, H. David}, year={2019}, month={Apr}, pages={456–465} }
 @article{cullen_jacob_cornish_vanderschel_cotter_cubeta_carbone_gilger_2019, title={Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States}, volume={14}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0214214}, DOI={10.1371/journal.pone.0214214}, abstractNote={Morphological characterization and multi-locus DNA sequence analysis of fungal isolates obtained from 32 clinical cases of equine fungal keratitis (FK) was performed to identify species and determine associations with antifungal susceptibility, response to therapy and clinical outcome. Two species of Aspergillus (A. flavus and A. fumigatus) and three species of Fusarium (F. falciforme, F. keratoplasticum, and F. proliferatum) were the most common fungi isolated and identified from FK horses. Most (91%) equine FK Fusarium nested within the Fusarium solani species complex (FSSC) with nine genetically diverse strains/lineages, while 83% of equine FK Aspergillus nested within the A. flavus clade with three genetically diverse lineages. Fungal species and evolutionary lineage were not associated with clinical outcome. However, species of equine FK Fusarium were more likely (p = 0.045) to be associated with stromal keratitis. Species of Aspergillus were more susceptible to voriconazole and terbinafine than species of Fusarium, while species of Fusarium were more susceptible to thiabendazole than species of Aspergillus. At the species level, A. fumigatus and A. flavus were more susceptible to voriconazole and terbinafine than F. falciforme. Natamycin susceptibility was higher for F. falciforme and A. fumigatus compared to A. flavus. Furthermore, F. falciforme was more susceptible to thiabendazole than A. flavus and A. fumigatus. These observed associations of antifungal sensitivity to natamycin, terbinafine, and thiabendazole demonstrate the importance of fungal identification to the species rather than genus level. The results of this study suggest that treatment of equine FK with antifungal agents requires accurate fungal species identification.}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Cullen, Megan and Jacob, Megan E. and Cornish, Vicki and VanderSchel, Ian Q. and Cotter, Henry Van T. and Cubeta, Marc A. and Carbone, Ignazio and Gilger, Brian C.}, editor={Kniemeyer, OlafEditor}, year={2019}, month={Mar}, pages={e0214214} }
 @article{carbone_white_miadlikowska_arnold_miller_magain_u'ren_lutzoni_2019, title={T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees}, volume={8}, ISSN={2576-098X}, url={http://dx.doi.org/10.1128/MRA.00328-19}, DOI={10.1128/MRA.00328-19}, abstractNote={The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.}, number={29}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={Carbone, Ignazio and White, James B. and Miadlikowska, Jolanta and Arnold, A. Elizabeth and Miller, Mark A. and Magain, Nicolas and U'Ren, Jana M. and Lutzoni, François}, editor={Cuomo, Christina A.Editor}, year={2019}, month={Jul} }
 @article{molo_heiniger_boerema_carbone_2019, title={Trial Summary on the Comparison of Various Non-Aflatoxigenic Strains of Aspergillus flavus on Mycotoxin Levels and Yield in Maize}, volume={111}, ISSN={["1435-0645"]}, DOI={10.2134/agronj2018.07.0473}, abstractNote={Core Ideas

Biocontrol strains are effective at reducing AF levels in maize.
Native and commercially available biocontrol strains are equally effective in reducing AF levels.
Deploying strains of opposite mating types in combination can lead to the greatest reduction in AF contamination.
}, number={2}, journal={AGRONOMY JOURNAL}, author={Molo, Megan S. and Heiniger, Ron W. and Boerema, Leah and Carbone, Ignazio}, year={2019}, pages={942–946} }
 @article{salgado-salazar_beirn_ismaiel_boehm_carbone_putman_tredway_clarke_crouch_2018, title={Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass}, volume={122}, ISSN={1878-6146}, url={http://dx.doi.org/10.1016/J.FUNBIO.2018.04.004}, DOI={10.1016/J.FUNBIO.2018.04.004}, abstractNote={Dollar spot is one of the most destructive and economically important fungal diseases of amenity turfgrasses. The causal agent was first described in 1937 as the ascomycete Sclerotinia homoeocarpa. However, the genus-level taxonomic placement of this fungus has been the subject of an ongoing debate for over 75 y. Existing morphological and rDNA sequence evidence indicates that this organism is more appropriately placed in the family Rutstroemiaceae rather than the Sclerotiniaceae. Here we use DNA sequence data from samples of the dollar spot fungus and other members of the Rutstroemiaceae (e.g. Rutstroemia, Lanzia, Lambertella) collected throughout the world to determine the generic identity of the turfgrass dollar spot pathogen. Phylogenetic evidence from three nucleotide sequence markers (CaM, ITS and Mcm7; 1810-bp) confirmed that S. homoeocarpa is not a species of Sclerotinia; nor is it a member of any known genus in the Rutstroemiaceae. These data support the establishment of a new genus, which we describe here as Clarireedia gen. nov. The type species for the genus, Clarireedia homoeocarpa comb. nov., is described to accommodate the dollar spot fungus, and a neotype is designated. Three new species in this clade, Clarireedia bennettii sp. nov., Clarireedia jacksonii sp. nov., and Clarireedia monteithiana sp. nov. that also cause dollar spot disease are described. Clarireedia homoeocarpa and C. bennettii occur primarily on Festuca rubra (C3 grass) hosts and appear to be restricted to the United Kingdom. Clarireedia jacksonii and C. monteithiana occur on a variety of C3 and C4 grass hosts, respectively, and appear to be globally distributed. This resolved taxonomy puts to rest a major controversy amongst plant pathologists and provides a foundation for better understanding the nature and biology of these destructive pathogens.}, number={8}, journal={Fungal Biology}, publisher={Elsevier BV}, author={Salgado-Salazar, Catalina and Beirn, Lisa A. and Ismaiel, Adnan and Boehm, Michael J. and Carbone, Ignazio and Putman, Alexander I. and Tredway, Lane P. and Clarke, Bruce B. and Crouch, Jo Anne}, year={2018}, month={Aug}, pages={761–773} }
 @article{ojiambo_battilani_cary_blum_carbone_2018, title={Cultural and Genetic Approaches to Manage Aflatoxin Contamination: Recent Insights Provide Opportunities for Improved Control}, volume={108}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/PHYTO-04-18-0134-RVW}, DOI={10.1094/PHYTO-04-18-0134-RVW}, abstractNote={ Aspergillus flavus is a morphologically complex species that can produce the group of polyketide derived carcinogenic and mutagenic secondary metabolites, aflatoxins, as well as other secondary metabolites such as cyclopiazonic acid and aflatrem. Aflatoxin causes aflatoxicosis when aflatoxins are ingested through contaminated food and feed. In addition, aflatoxin contamination is a major problem, from both an economic and health aspect, in developing countries, especially Asia and Africa, where cereals and peanuts are important food crops. Earlier measures for control of A. flavus infection and consequent aflatoxin contamination centered on creating unfavorable environments for the pathogen and destroying contaminated products. While development of atoxigenic (nonaflatoxin producing) strains of A. flavus as viable commercial biocontrol agents has marked a unique advance for control of aflatoxin contamination, particularly in Africa, new insights into the biology and sexuality of A. flavus are now providing opportunities to design improved atoxigenic strains for sustainable biological control of aflatoxin. Further, progress in the use of molecular technologies such as incorporation of antifungal genes in the host and host-induced gene silencing, is providing knowledge that could be harnessed to develop germplasm that is resistant to infection by A. flavus and aflatoxin contamination. This review summarizes the substantial progress that has been made to understand the biology of A. flavus and mitigate aflatoxin contamination with emphasis on maize. Concepts developed to date can provide a basis for future research efforts on the sustainable management of aflatoxin contamination. }, number={9}, journal={Phytopathology}, publisher={Scientific Societies}, author={Ojiambo, Peter S. and Battilani, Paola and Cary, Jeffrey W. and Blum, Burt H. and Carbone, Ignazio}, year={2018}, month={Sep}, pages={1024–1037} }
 @book{molo_heiniger_boerema_carbone_2018, place={Raleigh, NC}, title={Management practices for controlling mycotoxins in corn: A three-year summary}, url={http://content.ces.ncsu.edu/management-practices-for-controlling-mycotoxins-in-corn}, number={AG-852}, institution={North Carolina State University}, author={Molo, M. and Heiniger, R. and Boerema, L. and Carbone, I.}, year={2018} }
 @article{blanco-meneses_carbone_ristaino_2018, title={Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe}, volume={27}, ISSN={0962-1083}, url={http://dx.doi.org/10.1111/mec.14453}, DOI={10.1111/mec.14453}, abstractNote={Abstract}, number={3}, journal={Molecular Ecology}, publisher={Wiley}, author={Blanco-Meneses, Monica and Carbone, Ignazio and Ristaino, Jean B.}, year={2018}, month={Jan}, pages={737–751} }
 @article{drott_lazzaro_brown_carbone_milgroom_2017, title={Balancing selection for aflatoxin in
            Aspergillus flavus
            is maintained through interference competition with, and fungivory by insects}, volume={284}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2017.2408}, DOI={10.1098/rspb.2017.2408}, abstractNote={The role of microbial secondary metabolites in the ecology of the organisms that produce them remains poorly understood. Variation in aflatoxin production byAspergillus flavusis maintained by balancing selection, but the ecological function and impact on fungal fitness of this compound are unknown. We hypothesize that balancing selection for aflatoxin production inA. flavusis driven by interaction with insects. To test this, we competed naturally occurring aflatoxigenic and non-aflatoxigenic fungal isolates againstDrosophilalarvae on medium containing 0–1750 ppb aflatoxin, using quantitative PCR to quantifyA. flavusDNA as a proxy for fungal fitness. The addition of aflatoxin across this range resulted in a 26-fold increase in fungal fitness. With no added toxin, aflatoxigenic isolates caused higher mortality ofDrosophilalarvae and had slightly higher fitness than non-aflatoxigenic isolates. Additionally, aflatoxin production increased an average of 1.5-fold in the presence of a single larva and nearly threefold when the fungus was mechanically damaged. We argue that the role of aflatoxin in protection from fungivory is inextricably linked to its role in interference competition. Our results, to our knowledge, provide the first clear evidence of a fitness advantage conferred toA. flavusby aflatoxin when interacting with insects.}, number={1869}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Drott, Milton T. and Lazzaro, Brian P. and Brown, Dan L. and Carbone, Ignazio and Milgroom, Michael G.}, year={2017}, month={Dec}, pages={20172408} }
 @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{thomas_carbone_cohen_ojiambo_2017, title={Occurrence and Distribution of Mating Types of Pseudoperonospora cubensis in the United States}, volume={107}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/PHYTO-06-16-0236-R}, DOI={10.1094/phyto-06-16-0236-r}, abstractNote={ During the past two decades, a resurgence of cucurbit downy mildew has occurred around the world, resulting in severe disease epidemics. In the United States, resurgence of the disease occurred in 2004 and several hypotheses, including introduction of a new genetic recombinant or pathotype of the pathogen, have been suggested as potential causes for this resurgence. Occurrence and distribution of mating types of Pseudoperonospora cubensis in the United States were investigated using 40 isolates collected from cucurbits across 11 states from 2005 to 2013. Pairing of unknown isolates with known mating-type tester strains on detached leaves of cantaloupe or cucumber resulted in oospore formation 8 to 10 days after inoculation. Isolates differed in their ability to form oospores across all coinoculation pairings, with oospore numbers ranging from 280 to 1,000 oospores/cm2 of leaf tissue. Oospores were hyaline to golden-yellow, spherical, and approximately 36 μm in diameter. Of the 40 isolates tested, 24 were found to be of the A1 mating type, while 16 were of the A2 mating type. Mating type was significantly (P < 0.0001) associated with host type, whereby all isolates collected from cucumber were of the A1 mating type, while isolates from squash and watermelon were of the A2 mating type. Similarly, mating type was significantly (P = 0.0287) associated with geographical region, where isolates from northern-tier states of Michigan, New Jersey, New York, and Ohio were all A1, while isolates belonging to either A1 or A2 mating type were present in equal proportions in southern-tier states of Alabama, Florida, Georgia, North Carolina, South Carolina, and Texas. Viability assays showed that oospores were viable and, on average, approximately 40% of the oospores produced were viable as determined by the plasmolysis method. This study showed that A1 and A2 mating types of P. cubensis are present and the pathogen could potentially reproduce sexually in cucurbits within the United States. In addition, the production of viable oospores reported in this study suggests that oospores could have an important role in the biology of P. cubensis and could potentially influence the epidemiology of cucurbit downy mildew in the United States. }, number={3}, journal={Phytopathology}, publisher={Scientific Societies}, author={Thomas, Anna and Carbone, Ignazio and Cohen, Yigal and Ojiambo, Peter S.}, year={2017}, month={Mar}, pages={313–321} }
 @article{o’keeffe_carbone_jones_mitchell_2017, title={Plastic potential: how the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants}, volume={38}, ISSN={1369-5266}, url={http://dx.doi.org/10.1016/j.pbi.2017.04.014}, DOI={10.1016/j.pbi.2017.04.014}, abstractNote={Predicting the effects of plant-associated microbes on emergence, spread, and evolution of plant pathogens demands an understanding of how pathogens respond to these microbes at two levels of biological organization: that of an individual pathogen and that of a pathogen population across multiple individual plants. We first examine the plastic responses of individual plant pathogens to microbes within a shared host, as seen through changes in pathogen growth and multiplication. We then explore the limited understanding of how within-plant microbial interactions affect pathogen populations and discuss the need to incorporate population-level observations with population genomic techniques. Finally, we suggest that integrating across levels will further our understanding of the ecological and evolutionary impacts of within-plant microbial interactions on pathogens.}, journal={Current Opinion in Plant Biology}, publisher={Elsevier BV}, author={O’Keeffe, Kayleigh R and Carbone, Ignazio and Jones, Corbin D and Mitchell, Charles E}, year={2017}, month={Aug}, pages={78–83} }
 @article{thomas_carbone_choe_quesada-ocampo_ojiambo_2017, title={Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis}, volume={7}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.3194}, DOI={10.1002/ece3.3194}, abstractNote={Abstract}, number={16}, journal={Ecology and Evolution}, publisher={Wiley}, author={Thomas, Anna and Carbone, Ignazio and Choe, Kisurb and Quesada-Ocampo, Lina M. and Ojiambo, Peter S.}, year={2017}, month={Jul}, pages={6231–6246} }
 @article{thomas_carbone_lebeda_ojiambo_2017, title={Virulence Structure Within Populations of Pseudoperonospora cubensis in the United States}, volume={107}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-07-16-0277-r}, abstractNote={ Cucurbit downy mildew (CDM), caused by the obligate oomycete Pseudoperonospora cubensis, has resurged around the world during the past three decades. A new pathotype or genetic recombinant of P. cubensis have been suggested as possible reasons for the resurgence of CDM in the United States in 2004. In total, 22 isolates collected between 2004 and 2014, mainly in the eastern United States, were tested for their compatibility with a set of 15 cucurbit host types. The virulence structure within these isolates was evaluated on a set of 12 differential genotypes from eight genera. All isolates were highly compatible with the susceptible cultivar of Cucumis sativus, whereas the least compatibility was observed with Luffa cylindrica and Momordica charantia. Based on the compatibility with the differential host set, five pathotypes (1, 3, 4, 5, and 6) were identified among the 22 isolates examined. Pathotypes 1 and 3 had not been previously described in the United States and isolates of these two new pathotypes were also compatible with ‘Poinsett 76’, a cultivar of C. sativus known to be resistant to CDM prior to 2004. Virulence within the pathogen population was expressed based on virulence factors, virulence phenotypes, and virulence complexity. The number of virulence factors ranged from two to eight, indicating a complex virulence structure, with 77% of the isolates having five to eight virulence factors. Thirteen virulence phenotypes were identified; the mean number of virulence factors per isolate and mean number of virulence factors per virulence phenotype was 5.05 and 5.23, respectively, indicating that complex isolates and phenotypes contributed equally to the complex virulence structure of P. cubensis. Gleason and Shannon indices of diversity were 3.88 and 2.32, respectively, indicating a diverse virulence structure of P. cubensis within the United States population. The diverse virulence and high virulence complexity within the pathogen population indicate that host resistance alone in available cucurbit cultivars will not be effective to control CDM. An integrated approach involving a combination of fungicide application and introduction of cultivars with new resistance genes will be required for effective management of CDM. }, number={6}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Thomas, Anna and Carbone, Ignazio and Lebeda, Ales and Ojiambo, Peter S.}, year={2017}, month={Jun}, pages={777–785} }
 @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{carbone_white_miadlikowska_arnold_miller_kauff_u'ren_may_lutzoni_2016, title={T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life}, volume={33}, ISSN={1367-4803 1460-2059}, url={http://dx.doi.org/10.1093/bioinformatics/btw808}, DOI={10.1093/bioinformatics/btw808}, abstractNote={Abstract}, number={8}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Carbone, Ignazio and White, James B. and Miadlikowska, Jolanta and Arnold, A. Elizabeth and Miller, Mark A. and Kauff, Frank and U'Ren, Jana M. and May, Georgiana and Lutzoni, François}, year={2016}, month={Dec}, pages={btw808} }
 @article{putman_tredway_carbone_2015, title={Characterization and distribution of mating-type genes of the turfgrass pathogen Sclerotinia homoeocarpa on a global scale}, volume={81}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2015.05.012}, abstractNote={Sclerotinia homoeocarpa F.T. Bennett is a filamentous member of Ascomycota that causes dollar spot, the most economically important disease of turfgrass worldwide. We sequenced and characterized the mating-type (MAT) locus of four recently-collected contemporary strains causing dollar spot, four historical type strains used to describe the fungus, and three species of Rutstroemiaceae. Moreover, we developed a multiplex PCR assay to screen 1019 contemporary isolates for mating-type. The organization of the MAT loci of all strains examined could be classified into one of four categories: (1) putatively heterothallic, as exemplified by all contemporary strains and three of four historical type strains; (2) putatively heterothallic with a deleted putative gene in the MAT1-2 idiomorph, as detected in strains from two recently-collected populations in the United Kingdom that show more similarity to historical strains; (3) putatively homothallic with close physical linkage between MAT1-1-1 and MAT1-2-1, as found in one historical type strain of S. homoeocarpa and two strains of Rutstroemia cuniculi; and (4) an unresolved but apparently homothallic organization in which strains contained both MAT1-1-1 and MAT1-2-1 but linkage between these genes and between the two flanking genes could not be confirmed, as identified in R. paludosa and Poculum henningsianum. In contemporary S. homoeocarpa populations there was no significant difference in the frequency of the two mating types in clone-corrected samples when analyzed on regional and local scales, suggesting sex may be possible in this pathogen. However, two isolates from Italy and twenty from California were heterokaryotic for both complete heterothallic MAT idiomorphs. Results from this study contribute to knowledge about mating systems in filamentous fungi and enhance our understanding of the evolution and biology of an important plant pathogen.}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Putman, Alexander I. and Tredway, Lane P. and Carbone, Ignazio}, year={2015}, month={Aug}, pages={25–40} }
 @article{olarte_worthington_horn_moore_singh_monacell_dorner_stone_xie_carbone_2015, title={Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus}, volume={24}, ISSN={0962-1083}, url={http://dx.doi.org/10.1111/mec.13153}, DOI={10.1111/mec.13153}, abstractNote={Abstract}, number={8}, journal={Molecular Ecology}, publisher={Wiley}, author={Olarte, Rodrigo A. and Worthington, Carolyn J. and Horn, Bruce W. and Moore, Geromy G. and Singh, Rakhi and Monacell, James T. and Dorner, Joe W. and Stone, Eric A. and Xie, De-Yu and Carbone, Ignazio}, year={2015}, month={Apr}, pages={1889–1909} }
 @article{call_sun_yu_pearman_thomas_trigiano_carbone_xiang_2015, title={Genetic structure and post-glacial expansion ofCornus floridaL. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling}, volume={54}, ISSN={1674-4918}, url={http://dx.doi.org/10.1111/jse.12171}, DOI={10.1111/jse.12171}, abstractNote={Abstract}, number={2}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Call, Ashley and Sun, Yan-Xia and Yu, Yan and Pearman, Peter B. and Thomas, David T. and Trigiano, Robert N. and Carbone, Ignazio and Xiang, Qiu-Yun Jenny}, year={2015}, month={Sep}, pages={136–151} }
 @article{lassiter_russ_nusbaum_zeng_saville_olarte_carbone_hu_seguin-orlando_samaniego_et al._2015, title={Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species}, volume={61}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/s00294-015-0480-3}, DOI={10.1007/s00294-015-0480-3}, abstractNote={Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.}, number={4}, journal={Current Genetics}, publisher={Springer Science and Business Media LLC}, author={Lassiter, Erica S. and Russ, Carsten and Nusbaum, Chad and Zeng, Qiandong and Saville, Amanda C. and Olarte, Rodrigo A. and Carbone, Ignazio and Hu, Chia-Hui and Seguin-Orlando, Andaine and Samaniego, Jose A. and et al.}, year={2015}, month={Mar}, pages={567–577} }
 @article{runa_carbone_bhatnagar_payne_2015, title={Nuclear heterogeneity in conidial populations of Aspergillus flavus}, volume={84}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2015.09.003}, abstractNote={Aspergillus flavus is a major producer of aflatoxin and an opportunistic pathogen for a wide range of hosts. Understanding genotypic and phenotypic variation within strains of A. flavus is important for controlling disease and reducing aflatoxin contamination. A. flavus is multinucleate and predominantly haploid (n) and homokaryotic. Although cryptic heterokaryosis may occur in nature, it is unclear how nuclei in A. flavus influence genetic heterogeneity and if nuclear condition plays a role in fungal ecology. A. flavus mainly reproduces asexually by producing conidia. In order to observe whether conidia are homokaryotic or heterokaryotic, we labeled nuclei of A. flavus using two different nuclear localized fluorescent reporters. The reporter constructs (pYH2A and pCH2B), encode histones HH2A and HH2B fused at the C terminus with either yellow (EYFP) or cyan (ECFP) fluorescent proteins, respectively. The constructs were transformed into the double auxotrophic strain AFC-1 (−pyrG, −argD) to generate a strain containing each reporter construct. By taking advantage of the nutritional requirement for each strain, we were able to generate fusants between FR36 (−argD) expressing yellow fluorescence, and FR46 (−pyr4) expressing cyan fluorescence. Conidia from fusants between FR36 and FR46 showed three types of fluorescence: only EYFP, only ECFP or both EYFP + ECFP. Conidia containing nuclei expressing EYFP + ECFP were separated by Fluorescence-Activated Cell sorting (FACS) and were found to contain both yellow and cyan fluorescent markers in the same nucleus. Further characterization of conidia having only one nucleus but expressing both EYFP + ECFP fluorescence were found to be diploid (2n). Our findings suggest that A. flavus maintains nuclear heterogeneity in conidial populations.}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Runa, Farhana and Carbone, Ignazio and Bhatnagar, Deepak and Payne, Gary A.}, year={2015}, month={Nov}, pages={62–72} }
 @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} }
 @book{meyers_heiniger_boerema_carbone_2015, place={Raleigh, NC}, title={The Use of Management Practices to Reduce Mycotoxin Contamination in Corn}, number={AG-807}, institution={North Carolina Cooperative Extension Service}, author={Meyers, M. and Heiniger, R. and Boerema, L. and Carbone, I.}, year={2015} }
 @misc{putman_carbone_2014, title={Challenges in analysis and interpretation of microsatellite data for population genetic studies}, volume={4}, ISSN={["2045-7758"]}, DOI={10.1002/ece3.1305}, abstractNote={Abstract}, number={22}, journal={ECOLOGY AND EVOLUTION}, author={Putman, Alexander I. and Carbone, Ignazio}, year={2014}, month={Nov}, pages={4399–4428} }
 @article{oono_lutzoni_arnold_kaye_jana m. u'ren_may_carbone_2014, title={GENETIC VARIATION IN HORIZONTALLY TRANSMITTED FUNGAL ENDOPHYTES OF PINE NEEDLES REVEALS POPULATION STRUCTURE IN CRYPTIC SPECIES}, volume={101}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.1400141}, abstractNote={• Premise of the study: Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.}, number={8}, journal={AMERICAN JOURNAL OF BOTANY}, author={Oono, Ryoko and Lutzoni, Francois and Arnold, A. Elizabeth and Kaye, Laurel and Jana M. U'Ren and May, Georgiana and Carbone, Ignazio}, year={2014}, month={Aug}, pages={1362–1374} }
 @article{monacell_carbone_2014, title={Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics}, volume={30}, ISSN={1460-2059 1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btu055}, DOI={10.1093/bioinformatics/btu055}, abstractNote={Abstract}, number={10}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Monacell, James T. and Carbone, Ignazio}, year={2014}, month={Jan}, pages={1488–1490} }
 @misc{miller_schaafsma_bhatnagar_bondy_carbone_harris_harrison_munkvold_oswald_pestka_et al._2014, title={Mycotoxins that affect the North American agri-food sector: state of the art and directions for the future}, volume={7}, ISSN={["1875-0796"]}, DOI={10.3920/wmj2013.1624}, abstractNote={This paper summarises workshop discussions at the 5th international MYCORED meeting in Ottawa, Canada (June 2012) with over 200 participants representing academics, government and industry scientists, government officials and farming organisations (present in roughly equal proportions) from 27 countries. Workshops centred on how mycotoxins in food and feed affect value chains and trade in the region covered by the North American Free Trade Agreement. Crops are contaminated by one or more of five important mycotoxins in parts of Canada and the United States every year, and when contaminated food and feed are consumed in amounts above tolerable limits, human and animal health are at risk. Economic loss from such contamination includes reduced crop yield, grain quality, animal productivity and loss of domestic and export markets. A systematic effort by grain producers, primary, transfer, and terminal elevators, millers and food and feed processers is required to manage these contaminants along the value chain. Workshops discussed lessons learned from investments in plant genetics, fungal genomics, toxicology, analytical and sampling science, management strategies along the food and feed value chains and methods to ameliorate the effects of toxins in grain on animal production and on reducing the impact of mycotoxins on population health in developing countries. These discussions were used to develop a set of priorities and recommendations.}, number={1}, journal={WORLD MYCOTOXIN JOURNAL}, author={Miller, J. D. and Schaafsma, A. W. and Bhatnagar, D. and Bondy, G. and Carbone, I. and Harris, L. J. and Harrison, G. and Munkvold, G. P. and Oswald, I. P. and Pestka, J. J. and et al.}, year={2014}, month={Feb}, pages={63–82} }
 @article{barnes_wingfield_carbone_kirisits_wingfield_2014, title={Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity}, volume={4}, ISSN={["2045-7758"]}, DOI={10.1002/ece3.1200}, abstractNote={Abstract}, number={18}, journal={ECOLOGY AND EVOLUTION}, author={Barnes, Irene and Wingfield, Michael J. and Carbone, Ignazio and Kirisits, Thomas and Wingfield, Brenda D.}, year={2014}, month={Sep}, pages={3642–3661} }
 @article{horn_sorensen_lamb_sobolev_olarte_worthington_carbone_2014, title={Sexual Reproduction in Aspergillus flavus Sclerotia Naturally Produced in Corn}, volume={104}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-05-13-0129-r}, abstractNote={ Aspergillus flavus is the major producer of carcinogenic aflatoxins worldwide in crops. Populations of A. flavus are characterized by high genetic variation and the source of this variation is likely sexual reproduction. The fungus is heterothallic and laboratory crosses produce ascospore-bearing ascocarps embedded within sclerotia. However, the capacity for sexual reproduction in sclerotia naturally formed in crops has not been examined. Corn was grown for 3 years under different levels of drought stress at Shellman, GA, and sclerotia were recovered from 146 ears (0.6% of ears). Sclerotia of A. flavus L strain were dominant in 2010 and 2011 and sclerotia of A. flavus S strain were dominant in 2012. The incidence of S strain sclerotia in corn ears increased with decreasing water availability. Ascocarps were not detected in sclerotia at harvest but incubation of sclerotia on the surface of nonsterile soil in the laboratory resulted in the formation of viable ascospores in A. flavus L and S strains and in homothallic A. alliaceus. Ascospores were produced by section Flavi species in 6.1% of the 6,022 sclerotia (18 of 84 ears) in 2010, 0.1% of the 2,846 sclerotia (3 of 36 ears) in 2011, and 0.5% of the 3,106 sclerotia (5 of 26 ears) in 2012. For sexual reproduction to occur under field conditions, sclerotia may require an additional incubation period on soil following dispersal at crop harvest. }, number={1}, journal={PHYTOPATHOLOGY}, author={Horn, Bruce W. and Sorensen, Ronald B. and Lamb, Marshall C. and Sobolev, Victor S. and Olarte, Rodrigo A. and Worthington, Carolyn J. and Carbone, Ignazio}, year={2014}, month={Jan}, pages={75–85} }
 @article{jana m. u'ren_riddle_monacell_carbone_miadlikowska_arnold_2014, title={Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi}, volume={14}, ISSN={["1755-0998"]}, DOI={10.1111/1755-0998.12252}, abstractNote={Abstract}, number={5}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Jana M. U'Ren and Riddle, Jakob M. and Monacell, James T. and Carbone, Ignazio and Miadlikowska, Jolanta and Arnold, A. Elizabeth}, year={2014}, month={Sep}, pages={1032–1048} }
 @article{wei_ayub_chen_mccarthy_hou_carbone_xue_tyler-smith_2013, title={A calibrated human Y-chromosomal phylogeny based on resequencing}, volume={23}, ISSN={["1549-5469"]}, DOI={10.1101/gr.143198.112}, abstractNote={We have identified variants present in high-coverage complete sequences of 36 diverse human Y chromosomes from Africa, Europe, South Asia, East Asia, and the Americas, representing eight major haplogroups. After restricting our analysis to 8.97 Mb of the unique male-specific Y sequence, we identified 6662 high-confidence variants, including single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and indels. We constructed phylogenetic trees using these variants, or subsets of them, and recapitulated the known structure of the tree. Assuming a male mutation rate of 1 × 10−9 per base pair per year, the time depth of the tree (haplogroups A3-R) was ∼101,000–115,000 yr, and the lineages found outside Africa dated to 57,000–74,000 yr, both as expected. In addition, we dated a striking Paleolithic male lineage expansion to 41,000–52,000 yr ago and the node representing the major European Y lineage, R1b, to 4000–13,000 yr ago, supporting a Neolithic origin for these modern European Y chromosomes. In all, we provide a nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree.}, number={2}, journal={GENOME RESEARCH}, author={Wei, Wei and Ayub, Qasim and Chen, Yuan and McCarthy, Shane and Hou, Yiping and Carbone, Ignazio and Xue, Yali and Tyler-Smith, Chris}, year={2013}, month={Feb}, pages={388–395} }
 @article{putman_carbone_tredway_2013, title={Development and characterization of 14 microsatellite loci for the plant pathogenic fungus Sclerotinia homoeocarpa}, volume={13}, number={5}, journal={Molecular Ecology Resources}, author={Putman, A.I. and Carbone, I. and Tredway, L.P.}, year={2013}, pages={966–968} }
 @article{bradshaw_slot_moore_chettri_wit_ehrlich_ganley_olson_rokas_carbone_et al._2013, title={Fragmentation of an aflatoxin-like gene cluster in a forest pathogen}, volume={198}, ISSN={["1469-8137"]}, DOI={10.1111/nph.12161}, abstractNote={Summary}, number={2}, journal={NEW PHYTOLOGIST}, author={Bradshaw, Rosie E. and Slot, Jason C. and Moore, Geromy G. and Chettri, Pranav and Wit, Pierre J. G. M. and Ehrlich, Kenneth C. and Ganley, Austen R. D. and Olson, Malin A. and Rokas, Antonis and Carbone, Ignazio and et al.}, year={2013}, month={Apr}, pages={525–535} }
 @article{agostini_albaladejo_aparicio_arthofer_berrebi_boag_carbone_conroy_cortesero_goncalves_et al._2013, title={Permanent genetic resources added to molecular ecology resources database 1 April 2013-31 May 2013}, volume={13}, number={5}, journal={Molecular Ecology Resources}, author={Agostini, C. and Albaladejo, R. G. and Aparicio, A. and Arthofer, W. and Berrebi, P. and Boag, P. T. and Carbone, I. and Conroy, G. C. and Cortesero, A. M. and Goncalves, E. C. and et al.}, year={2013}, pages={966–968} }
 @article{horn_olarte_peterson_carbone_2013, title={Sexual reproduction in Aspergillus tubingensis from section Nigri}, volume={105}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.3852/13-101}, DOI={10.3852/13-101}, abstractNote={A sclerotium-forming member of Aspergillus section Nigri was sampled from a population in a single field in North Carolina, USA, and identified as A. tubingensis based on genealogical concordance analysis. Aspergillus tubingensis was shown to be heterothallic, with individual strains containing either a MAT1-1 or MAT1-2 mating-type gene. Strains of opposite mating type were crossed on mixed cereal agar and incubated for 5–6 months. Stromata typically formed 1–2 indehiscent ascocarps containing asci and ascospores within the pseudo-parenchymatous matrix in a manner similar to the Petromyces sexual stage from section Flavi, which is closely related to section Nigri. Ascospores of A. tubingensis differed from those of section Flavi species in the reticulate ornamentation of ascospores and the presence of two crests that form an equatorial furrow. Sexual reproduction in A. tubingensis may be useful for enhancing enzyme and organic acid production through recombination-mediated genetic engineering of industrial strains.}, number={5}, journal={Mycologia}, publisher={Informa UK Limited}, author={Horn, Bruce W. and Olarte, Rodrigo A. and Peterson, Stephen W. and Carbone, Ignazio}, year={2013}, month={Sep}, pages={1153–1163} }
 @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} }
 @book{beirn_clarke_tredway_carbone_boehm_orshinsky_crouch_2012, title={Renaming the dollar spot fungus}, institution={Golf Course Management Current Research}, author={Beirn, L. and Clarke, B.B. and Tredway, L. and Carbone, I. and Boehm, MJ and Orshinsky, A.M. and Crouch, J.}, year={2012} }
 @article{arnold_carbone_lutzoni_may_2011, title={A multidimensional study of endophytic fungal diversity}, volume={2}, number={1}, journal={IMA Fungus}, author={Arnold, A.E. and Carbone, I. and Lutzoni, F. and May, G.}, year={2011}, pages={2–4} }
 @article{wu_bhatnagar_bui-klimke_carbone_hellmich_munkvold_paul_payne_takle_2011, title={Climate change impacts on mycotoxin risks in US maize}, volume={4}, ISSN={1875-0710 1875-0796}, url={http://dx.doi.org/10.3920/wmj2010.1246}, DOI={10.3920/wmj2010.1246}, abstractNote={To ensure future food security, it is crucial to understand how potential climate change scenarios will affect
agriculture. One key area of interest is how climatic factors, both in the near- and the long-term future, could affect
fungal infection of crops and mycotoxin production by these fungi. The objective of this paper is to review the
potential impact of climate change on three important mycotoxins that contaminate maize in the United States,
and to highlight key research questions and approaches for understanding this impact. Recent climate change
analyses that pertain to agriculture and in particular to mycotoxigenic fungi are discussed, with respect to the
climatic factors – temperature and relative humidity – at which they thrive and cause severe damage. Additionally,
we discuss how climate change will likely alter the life cycles and geographic distribution of insects that are known
to facilitate fungal infection of crops.}, number={1}, journal={World Mycotoxin Journal}, publisher={Wageningen Academic Publishers}, author={Wu, F. and Bhatnagar, D. and Bui-Klimke, T. and Carbone, I. and Hellmich, R. and Munkvold, G. and Paul, P. and Payne, G. and Takle, E.}, year={2011}, month={Jan}, pages={79–93} }
 @article{litvintseva_carbone_rossouw_thakur_govender_mitchell_2011, title={Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa}, volume={6}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0019688}, DOI={10.1371/journal.pone.0019688}, abstractNote={Most of the species of fungi that cause disease in mammals, including Cryptococcus neoformans var. grubii (serotype A), are exogenous and non-contagious. Cryptococcus neoformans var. grubii is associated worldwide with avian and arboreal habitats. This airborne, opportunistic pathogen is profoundly neurotropic and the leading cause of fungal meningitis. Patients with HIV/AIDS have been ravaged by cryptococcosis – an estimated one million new cases occur each year, and mortality approaches 50%. Using phylogenetic and population genetic analyses, we present evidence that C. neoformans var. grubii may have evolved from a diverse population in southern Africa. Our ecological studies support the hypothesis that a few of these strains acquired a new environmental reservoir, the excreta of feral pigeons (Columba livia), and were globally dispersed by the migration of birds and humans. This investigation also discovered a novel arboreal reservoir for highly diverse strains of C. neoformans var. grubii that are restricted to southern Africa, the mopane tree (Colophospermum mopane). This finding may have significant public health implications because these primal strains have optimal potential for evolution and because mopane trees contribute to the local economy as a source of timber, folkloric remedies and the edible mopane worm.}, number={5}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Litvintseva, Anastasia P. and Carbone, Ignazio and Rossouw, Jenny and Thakur, Rameshwari and Govender, Nelesh P. and Mitchell, Thomas G.}, editor={Nielsen, KirstenEditor}, year={2011}, month={May}, pages={e19688} }
 @article{olson_carbone_benson_2011, title={Phylogenetic history of Phytophthora cryptogea and P. drechsleri Isolates from floriculture crops in North Carolina greenhouses}, volume={101}, number={11}, journal={Phytopathology}, author={Olson, H. A. and Carbone, I. and Benson, D. M.}, year={2011}, pages={1373–1384} }
 @article{kaye_moyer_parks_carbone_cubeta_2011, title={Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia}, volume={101}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-01-10-0035}, abstractNote={ Exploring the genetic diversity and evolutionary history of plant viruses is critical to understanding their ecology and epidemiology. In this study, maximum-likelihood and population genetics-based methods were used to investigate the population structure, genetic diversity, and sources of genetic variation in field isolates of Tomato spotted wilt virus (TSWV) from peanut in North Carolina and Virginia. Selected regions of the nucleocapsid, movement, and RNA-dependent RNA polymerase genes were amplified and sequenced to identify haplotypes and infer genetic relationships between isolates of TSWV with heuristic methods. The haplotype structure of each locus consisted of 1 or 2 predominant haplotypes and >100 haplotypes represented by a single isolate. No specific haplotypes were associated with geographic area, peanut cultivar, or year of isolation. The population was panmictic at the regional level and high levels of genetic diversity were observed among isolates. There was evidence for positive selection on single amino acids in each gene on a background of predominant purifying selection acting upon each locus. The results of compatibility analyses and the persistence of specific gene sequences in isolates collected over three field seasons suggest that recombination was occurring in the population. Estimates of the population mutation rate suggest that mutation has had a significant effect on the shaping of this population and, together with purifying selection, these forces have been the predominant evolutionary forces influencing the TSWV population in peanut in North Carolina and Virginia. }, number={1}, journal={PHYTOPATHOLOGY}, author={Kaye, A. C. and Moyer, J. W. and Parks, E. J. and Carbone, I. and Cubeta, M. A.}, year={2011}, month={Jan}, pages={147–153} }
 @article{abbas_weaver_horn_carbone_monacell_shier_2011, title={Selection of Aspergillus flavus isolates for biological control of aflatoxins in corn}, volume={30}, ISSN={["1556-9551"]}, DOI={10.3109/15569543.2011.591539}, abstractNote={The fungus Aspergillus flavus is responsible for producing carcinogenic mycotoxins, the aflatoxins, on corn (maize) and other crops. An additional harmful toxin, cyclopiazonic acid, is produced by some isolates of A. flavus. Several A. flavus strains that do not produce one or both of these mycotoxins are being used in biological control to competitively exclude the toxin-producing strains from the agroecosystem, particularly from seeds, grain and other marketable commodities. Three well-studied non-aflatoxigenic strains, including two that are commercially available, have been compared in side-by-side field trials. The results of that study, together with a growing understanding of A. flavus ecology and new genetic insights, are guiding the selection of biocontrol strains and influencing crop management decisions for safe and sustainable production.}, number={2-3}, journal={TOXIN REVIEWS}, author={Abbas, Hamed K. and Weaver, Mark A. and Horn, Bruce W. and Carbone, Ignazio and Monacell, James T. and Shier, W. Thomas}, year={2011}, pages={59–70} }
 @article{horn_moore_carbone_2011, title={Sexual reproduction in aflatoxin-producing Aspergillus nomius}, volume={103}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.3852/10-115}, DOI={10.3852/10-115}, abstractNote={Sexual reproduction was examined in the aflatoxin-producing fungus Aspergillus nomius. Crosses between sexually compatible strains resulted in the formation of multiple nonostiolate ascocarps within stromata, which places the teleomorph in genus Petromyces. Ascocarp and ascospore morphology in Petromyces nomius were similar to that in P. flavus and P. parasiticus, and differences between teleomorphs were insufficient for species separation. Formation of mature ascocarps was infrequent, with only 24% of the 83 crosses producing viable ascospores. The majority of P. nomius strains contained a single mating-type gene (MAT1-1 or MAT1-2), but several strains contained both genes. MAT1-1/MAT1-2 strains were self-sterile and capable of mating with both MAT1-1 and MAT1-2 strains; hence P. nomius appears to be functionally heterothallic.}, number={1}, journal={Mycologia}, publisher={Informa UK Limited}, author={Horn, Bruce W. and Moore, Geromy G. and Carbone, Ignazio}, year={2011}, month={Jan}, pages={174–183} }
 @inbook{moore_beltz_carbone_ehrlich_horn_2011, title={The Population Dynamics of Aflatoxigenic Aspergilli}, ISBN={9789533073958}, url={http://www.intechopen.com/articles/show/title/the-population-dynamics-of-aflatoxigenic-aspergilli}, DOI={10.5772/23698}, abstractNote={Geromy G. Moore1, Shannon B. Beltz1, Ignazio Carbone2, Kenneth C. Ehrlich1 and Bruce W. Horn3 1United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana 2Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 3United States Department of Agriculture, Agricultural Research Service, National Peanut Research Laboratory, Dawson, Georgia United States of America}, booktitle={Aflatoxins - Biochemistry and Molecular Biology}, publisher={InTech}, author={Moore, Geromy G. and Beltz, Shannon B. and Carbone, Ignazio and Ehrlich, Kenneth C. and Horn, Bruce W.}, editor={Guevara-González, Ramón GerardoEditor}, year={2011}, month={Oct} }
 @inproceedings{goss_larsen_carbone_givens_chastagner_grünwald_frankel_kliejunas_palmieri_2010, place={Albany, CA}, title={Population genetic analysis reveals ancient evolution and recent migration of P. ramorum}, url={https://www.fs.usda.gov/treesearch/pubs/35074}, DOI={10.2737/psw-gtr-229}, abstractNote={The Sudden Oak Death Fourth Science Symposium provided a forum for current research on sudden oak death, caused by the exotic, quarantine pathogen, Phytophthora ramorum. Ninety submissions describing papers or posters on the following sudden oak death/P. ramorum topics are included: biology, genetics, nursery and wildland management, monitoring, ecology, and diagnostics.}, booktitle={Proceedings of the Sudden Oak Death Fourth Science Symposium}, publisher={U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station}, author={Goss, E.M. and Larsen, M. and Carbone, I.Givens and Givens, D.R. and Chastagner, G.A. and Grünwald, N.J. and Frankel, Susan J. and Kliejunas, John T. and Palmieri, Katharine M.}, editor={Frankel, S.J. and Kliejunas, J.T. and Palmieri, K.M.Editors}, year={2010}, pages={116–118} }
 @article{goss_carbone_grunwald_2009, title={Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum}, volume={18}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2009.04089.x}, abstractNote={Abstract}, number={6}, journal={MOLECULAR ECOLOGY}, author={Goss, E. M. and Carbone, I. and Grunwald, N. J.}, year={2009}, month={Mar}, pages={1161–1174} }
 @article{lourenco_moya_gonzalez-candelas_carbone_maffia_mizubuti_2009, title={Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches}, volume={99}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-99-6-0765}, abstractNote={ Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure. }, number={6}, journal={PHYTOPATHOLOGY}, author={Lourenco, Valdir, Jr. and Moya, Andres and Gonzalez-Candelas, Fernando and Carbone, Ignazio and Maffia, Luiz A. and Mizubuti, Eduardo S. G.}, year={2009}, month={Jun}, pages={765–774} }
 @article{parks_carbone_murphy_cowger_2009, title={Population Genetic Analysis of an Eastern US Wheat Powdery Mildew Population Reveals Geographic Subdivision and Recent Common Ancestry with UK and Israeli Populations}, volume={99}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-99-7-0840}, abstractNote={ The structure of the U.S. wheat powdery mildew population (Blumeria graminis f. sp. tritici) has not been previously investigated, and the global evolutionary history of B. graminis f. sp. tritici is largely unknown. After gathering 141 single-ascosporic B. graminis f. sp. tritici isolates from 10 eastern U.S. locations, 34 isolates from the United Kingdom, and 28 isolates from Israel, we analyzed pathogen population structure using presumptively neutral markers. DNA was extracted from conidia, primers for 12 “housekeeping” genes were designed, and amplicons were examined for polymorphism. Four genes were found to contain a total of 12 single-nucleotide polymorphisms in the U.S. population and were also analyzed in the U.K. and Israeli populations. In total, 25 haplotypes were inferred from the four concatenated genes, with 2 haplotypes comprising over 70% of the U.S. population. Using Hudson's tests and analysis of molecular variance, we found the wheat mildew isolates subdivided into four groups corresponding to distinct regions: the mid-Atlantic United States, the southern United States, the United Kingdom, and Israel. Genotypic diversity was greatest in samples from the United Kingdom, Israel, Virginia, and Kinston, NC. Using rarefaction, a procedure that compensates for differing sample sizes when estimating population richness and diversity, we found that cooler locations with greater conduciveness to regular powdery mildew epidemics had the greatest haplotype richness. Our results suggest that the eastern U.S. B. graminis f. sp. tritici population is young, descended recently from Old World populations with isolation and genetic drift, and is currently subdivided into northern and southern subpopulations. }, number={7}, journal={PHYTOPATHOLOGY}, author={Parks, Ryan and Carbone, Ignazio and Murphy, J. Paul and Cowger, Christina}, year={2009}, month={Jul}, pages={840–849} }
 @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} }
 @article{horn_ramirez-prado_carbone_2009, title={Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus}, volume={46}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2008.11.004}, abstractNote={The fungal phylum Ascomycota comprises a large proportion of species with no known sexual stage, despite high genetic variability in field populations. One such asexual species, Aspergillus parasiticus, is a potent producer of carcinogenic and hepatotoxic aflatoxins, polyketide-derived secondary metabolites that contaminate a wide variety of agricultural crops. In this study, individuals of A. parasiticus from a population showing an evolutionary history of recombination were examined for sexual reproduction. Crosses between strains with opposite mating-type genes MAT1-1 and MAT1-2 resulted in the development of ascospore-bearing ascocarps embedded within stromata. Sexually compatible strains belonged to different vegetative compatibility groups. Recombination through the independent assortment of chromosomes 3 and 6 was detected using loci for mating type, aflatoxin gene cluster, and a protein-encoding gene. Our discovery of the sexual stage in A. parasiticus has important implications for current biological control strategies using nontoxigenic strains to reduce aflatoxin contamination in crops.}, number={2}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Horn, Bruce W. and Ramirez-Prado, Jorge H. and Carbone, Ignazio}, year={2009}, month={Feb}, pages={169–175} }
 @article{horn_moore_carbone_2009, title={Sexual reproduction in Aspergillus flavus}, volume={101}, ISSN={["1557-2536"]}, DOI={10.3852/09-011}, abstractNote={Aspergillus flavus is the major producer of carcinogenic aflatoxins in crops worldwide and is also an important opportunistic human pathogen in aspergillosis. The sexual state of this heterothallic fungus is described from crosses between strains of the opposite mating type. Sexual reproduction occurred between sexually compatible strains belonging to different vegetative compatibility groups. Multiple, indehiscent ascocarps containing asci and ascospores formed within the pseudoparenchymatous matrix of stromata, which places the fungus in genus Petromyces. The teleomorph of P. flavus could not be distinguished from that of P. parasiticus (anamorph = A. parasiticus), another aflatoxin-producing species, based on morphology of the sexual structures. The two species can be separated by anamorph morphology, mycotoxin profile and molecular characters.}, number={3}, journal={MYCOLOGIA}, author={Horn, Bruce W. and Moore, Geromy G. and Carbone, Ignazio}, year={2009}, pages={423–429} }
 @article{horn_ramirez-prado_carbone_2009, title={The sexual state of Aspergillus parasiticus}, volume={101}, ISSN={["1557-2536"]}, DOI={10.3852/08-205}, abstractNote={The sexual state of Aspergillus parasiticus, a potent aflatoxin-producing fungus within section Flavi, is described. The production of nonostiolate ascocarps surrounded by a separate peridium within the stroma places the teleomorph in genus Petromyces. Petromyces parasiticus differs from P. alliaceus by its larger ascospores with finely tuberculate ornamentation. The anamorphic Aspergillus states of the two species differ in conidial head color and microscopic characters.}, number={2}, journal={MYCOLOGIA}, author={Horn, Bruce W. and Ramirez-Prado, Jorge H. and Carbone, Ignazio}, year={2009}, pages={275–280} }
 @article{powell_conant_brown_carbone_dean_2008, title={Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens}, volume={9}, ISSN={["1471-2164"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-42549135491&partnerID=MN8TOARS}, DOI={10.1186/1471-2164-9-147}, abstractNote={Abstract}, journal={BMC GENOMICS}, author={Powell, Amy J. and Conant, Gavin C. and Brown, Douglas E. and Carbone, Ignazio and Dean, Ralph A.}, year={2008}, month={Mar} }
 @article{ramirez-prado_moore_horn_carbone_2008, title={Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus}, volume={45}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2008.06.007}, abstractNote={We characterize the mating-type genes in Aspergillus flavus,Aspergillus parasiticus and Petromyces alliaceus. A single MAT1-1 or MAT1-2 gene was detected in the genomes of A. flavus and A. parasiticus, which is consistent with a potential heterothallic organization of MAT genes in these species. In contrast, the only known, functionally homothallic species in Aspergillus section Flavi, P. alliaceus, has tightly linked (<2kb) MAT1-1 and MAT1-2 genes, typical of other self-fertile homothallic euascomycetes. This is the first example of linked MAT genes within a homothallic species of Aspergillus. We tested the null hypothesis of no significant difference in the frequency of MAT1-1 and MAT1-2 in A. flavus and A. parasiticus sampled from a single peanut field in Georgia. For each species, mating-type frequencies were determined for the total population samples and for samples that were clone-corrected based on vegetative compatibility groups (VCGs) and aflatoxin gene cluster haplotypes. There was no significant difference in the frequency of the two mating types for A. flavus and A. parasiticus in either VCG or haplotype clone-corrected samples. The existence of both mating-type genes in equal proportions in A. flavus and A. parasiticus populations, coupled with their expression at the mRNA level and the high amino acid sequence identity of MAT1-1 (77%) and MAT1-2 (83%) with corresponding homologs in P. alliaceus, indicates the potential functionality of these genes and the possible existence of a sexual state in these agriculturally important species.}, number={9}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Ramirez-Prado, Jorge H. and Moore, Geromy G. and Horn, Bruce W. and Carbone, Ignazio}, year={2008}, month={Sep}, pages={1292–1299} }
 @article{clark_carbone_2008, title={Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer}, volume={38}, ISSN={["1208-6037"]}, DOI={10.1139/X07-209}, abstractNote={Genealogy based methods were used to estimate phylogeographic history for a Tasmanian endemic conifer, Huon pine ( Lagarostrobos franklinii (Hook. f.) Quinn). DNA from trees in eight populations was sequenced using three chloroplast primers (trnS–trnT, trnD–trnT, and psbC–trnS). Mean nucleotide diversity was low (π = 0.000 93 ± 0.000 06) from 892 base pairs of sequence, but varied in stands from 0.0 to 0.001 15. Two of the five haplotypes were widely distributed, but the most frequently occurring haplotype was found only in the western portion of the range. Population structure was highly significant among populations overall (GST= 0.261, where GSTis the coefficient of gene differentiation, and p ≤ 0.0001), and there were indications of significant isolation by distance (p ≤ 0.022). Populations exhibited the highest levels of differentiation between the southeastern and northwestern watersheds. Estimates of migration between populations obtained using both parametric and nonparametric methods indicated levels of gene flow consistent with an isolation by distance model. Nested clade analysis demonstrated a pattern of genetic diversity in Huon pine that is consistent with a history of range expansion. The exceptionally low level of nucleotide diversity, haplotype distribution, and paleoecological data are congruent with a history of long-term range reduction, population bottlenecks, and subsequent colonization events from refugial areas.}, number={6}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Clark, Catherine M. and Carbone, Ignazio}, year={2008}, month={Jun}, pages={1576–1589} }
 @article{brown_powell_carbone_dean_2008, title={GT-Miner: a graph-theoretic data miner, viewer, and model processor}, volume={3}, ISSN={0973-8894 0973-2063}, url={http://dx.doi.org/10.6026/97320630003235}, DOI={10.6026/97320630003235}, abstractNote={Inexpensive computational power combined with high-throughput experimental platforms has created a wealth of biological information requiring analytical tools and techniques for interpretation. Graph-theoretic concepts and tools have provided an important foundation for information visualization, integration, and analysis of datasets, but they have often been relegated to background analysis tasks. GT-Miner is designed for visual data analysis and mining operations, interacts with other software, including databases, and works with diverse data types. It facilitates a discovery-oriented approach to data mining wherein exploration of alterations of the data and variations of the visualization is encouraged. The user is presented with a basic iterative process, consisting of loading, visualizing, transforming, and then storing the resultant information. Complex analyses are built-up through repeated iterations and user interactions. The iterative process is optimized by automatic layout following transformations and by maintaining a current selection set of interest for elements modified by the transformations. Multiple visualizations are supported including hierarchical, spring, and force-directed self-organizing layouts. Graphs can be transformed with an extensible set of algorithms or manually with an integral visual editor. GT-Miner is intended to allow easier access to visual data mining for the non-expert. Availability The GT-Miner program and supplemental materials, including example uses and a user guide, are freely available from http://www.cifr.ncsu.edu/bioinformatics/downloads/}, number={5}, journal={Bioinformation}, publisher={Biomedical Informatics}, author={Brown, Douglas E. and Powell, Amy J. and Carbone, Ignazio and Dean, Ralph A.}, year={2008}, month={Dec}, pages={235–237} }
 @article{charlton_carbone_tavantzis_cubeta_2008, title={Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi}, volume={100}, ISSN={["0027-5514"]}, DOI={10.3852/07-108R}, abstractNote={Isolates from closely related fungi in the Rhizoctonia species complex were examined for the occurrence of the M2 double-stranded RNA (dsRNA) by amplifying a conserved 1000 nucleotide region of the dsRNA with reverse transcription PCR. The M2 dsRNA was detected in representative isolates belonging to three anastomosis groups (AG) of R. solani (AG-1-IA, AG-4 and AG-6; teleomorph = Thanatephorus) and four AGs of binucleate Rhizoctonia (AGA, AG-F, AG-R and AG-U; teleomorph = Ceratobasidium). Amplified PCR products from the 3′ region of the M2 dsRNA from a representative sample of 12 isolates from eight different AGs were sequenced and subjected to parsimony analysis and coalescent simulations to infer ancestral lineages and to reconstruct the ancestral history of haplotypes. Seven dsRNA haplotypes were inferred from the sample of 12 isolates. One haplotype was composed of only isolates of Ceratobasidium belonging to different AGs. The rooted gene genealogies from coalescent simulations suggested that the ancestral M2 dsRNA haplotype most likely evolved in Thanatephorus (anamorph = R. solani AG-1-IA) and has been acquired recently by isolates of Ceratobasidium. Reconstruction of the ancestral history of haplotypes with a parsimony-based approach that assumes both mutation and recombination suggested that four haplotypes recombined before coalescing to their most recent common ancestor, while three haplotypes coalesced without recombination in the recent past. There was no unique association of haplotype within a specific AG of either Ceratobasidium or Thanatephorus to support co-evolution of the M2 dsRNA within the fungal host. To our knowledge this is the first report of a dsRNA occurring in Ceratobasidium that also is present in Thanatephorus.}, number={4}, journal={MYCOLOGIA}, author={Charlton, Nikki D. and Carbone, Ignazio and Tavantzis, Stellos M. and Cubeta, Marc A.}, year={2008}, pages={555–564} }
 @article{parks_carbone_murphy_marshall_cowger_2008, title={Virulence structure of the Eastern US wheat powdery mildew population}, volume={92}, ISSN={["0191-2917"]}, DOI={10.1094/PDIS-92-7-1074}, abstractNote={ Little is known about the population structure of wheat powdery mildew in the eastern United States, and the most recent report on virulence in this population involved isolates collected in 1993–94. In the present study, wheat leaves naturally infected with powdery mildew were collected from 10 locations in the southeastern United States in 2003 and 2005 and a collection of 207 isolates was derived from single ascospores. Frequencies of virulence to 16 mildew resistance (Pm) genes were determined by inoculating the isolates individually on replicated plates of detached leaves of differential wheat lines. These virulence frequencies were used to infer local effectiveness of Pm genes, estimate virulence complexity, detect significant associations between pairs of pathogen avirulence loci, and assess whether phenotypic differences between pathogen subpopulations increased with geographic distance. In both years, virulence to Pm3a, Pm3c, Pm5a, and Pm7 was present in more than 90% of sampled isolates and virulence to Pm1a, Pm16, Pm17, and Pm25 was present in fewer than 10% of isolates. In each year, 71 to 88% of all sampled isolates possessed one of a few multilocus virulence phenotypes, although there were significant differences among locations in frequencies of virulence to individual Pm genes. Several significant associations were detected between alleles for avirulence to pairs of Pm genes. Genetic (phenotypic) distance between isolate subpopulations increased significantly (R2 = 0.40, P < 0.001) with increasing geographic separation; possible explanations include different commercial deployment of Pm genes and restricted gene flow in the pathogen population. }, number={7}, journal={PLANT DISEASE}, author={Parks, Ryan and Carbone, Ignazio and Murphy, J. Paul and Marshall, David and Cowger, Christina}, year={2008}, month={Jul}, pages={1074–1082} }
 @article{gomez-alpizar_carbone_ristaino_2007, title={An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies}, volume={104}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33847647990&partnerID=MN8TOARS}, DOI={10.1073/pnas.0611479104}, abstractNote={
            Phytophthora infestans
            (Mont.) de Bary caused the 19th century Irish Potato Famine. We assessed the genealogical history of
            P. infestans
            using sequences from portions of two nuclear genes (β-
            tubulin
            and
            Ras
            ) and several mitochondrial loci P3, (
            rpl
            14,
            rpl
            5, tRNA) and P4 (
            Cox1
            ) from 94 isolates from South, Central, and North America, as well as Ireland. Summary statistics, migration analyses and the genealogy of current populations of
            P. infestans
            for both nuclear and mitochondrial loci are consistent with an “out of South America” origin for
            P. infestans
            . Mexican populations of
            P. infestans
            from the putative center of origin in Toluca Mexico harbored less nucleotide and haplotype diversity than Andean populations. Coalescent-based genealogies of all loci were congruent and demonstrate the existence of two lineages leading to present day haplotypes of
            P. infestans
            on potatoes. The oldest lineage associated with isolates from the section Anarrhichomenun including
            Solanum tetrapetalum
            from Ecuador was identified as
            Phytophthora andina
            and evolved from a common ancestor of
            P. infestans
            . Nuclear and mitochondrial haplotypes found in Toluca Mexico were derived from only one of the two lineages, whereas haplotypes from Andean populations in Peru and Ecuador were derived from both lineages. Haplotypes found in populations from the U.S. and Ireland was derived from both ancestral lineages that occur in South America suggesting a common ancestry among these populations. The geographic distribution of mutations on the rooted gene genealogies demonstrate that the oldest mutations in
            P. infestans
            originated in South America and are consistent with a South American origin.
          }, number={9}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Gomez-Alpizar, Luis and Carbone, Ignazio and Ristaino, Jean Beagle}, year={2007}, month={Feb}, pages={3306–3311} }
 @article{carbone_ramirez-prado_jakobek_horn_2007, title={Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster}, volume={7}, ISSN={["1471-2148"]}, DOI={10.1186/1471-2148-7-111}, abstractNote={The biosynthesis of aflatoxin (AF) involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST) and O-methylsterigmatocystin (OMST), the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A. nidulans that synthesizes only ST, A. flavus that makes predominantly AF, and A. parasiticus that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of Aspergillus.To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL). With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species.Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE) or the copies may partition the ancestral function (aflA/aflB). In some gene modules, the duplicated copy may simply augment/supplement a specific pathway function (aflR/aflS and aflX/aflY) or the duplicated copy may evolve a completely new function (aflT/aflQ and aflC/aflW). Gene modules that are contiguous in one species and noncontiguous in others point to possible rearrangements of cluster genes in the evolution of these species. Significantly higher mean Ka/Ks values in section Flavi compared to non-section Flavi species indicate increased positive selection acting in the evolution of genes in OMST and AF gene clusters.}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Carbone, Ignazio and Ramirez-Prado, Jorge H. and Jakobek, Judy L. and Horn, Bruce W.}, year={2007}, month={Jul} }
 @article{moser_carbone_arasu_gibson_2007, title={Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancylostoma caninum)}, volume={93}, ISSN={["1937-2345"]}, DOI={10.1645/GE-1096R.1}, abstractNote={Ancylostoma caninum is a globally distributed canine parasitic nematode. To test whether positive selection, population structure, or both affect genetic variation at the candidate vaccine target Ancylostoma secreted protein 1 (asp-1), we have quantified the genetic variation in A. caninum at asp-1 and a mitochondrial gene, cytochrome oxidase subunit 1 (cox-1), using the statistical population analysis tools found in the SNAP Workbench. The mitochondrial gene cox-1 exhibits moderate diversity within 2 North American samples, comparable to the level of variation observed in other parasitic nematodes. The protein coding portion for the C-terminal half of asp-1 shows similar levels of genetic variation in a Wake County, North Carolina, sample as cox-1. Standard tests of neutrality provide little formal evidence for selection acting on this locus, but haplotype networks for 2 of the exon regions have significantly different topologies, consistent with different evolutionary forces shaping variation at either end of a 1.3-kilobase stretch of sequence. Evidence for gene flow among geographically distinct samples suggests that the mobility of hosts of A. caninum is an important contributing factor to the population structure of the parasite.}, number={4}, journal={JOURNAL OF PARASITOLOGY}, author={Moser, Jennifer M. and Carbone, Ignazio and Arasu, Prema and Gibson, Greg}, year={2007}, month={Aug}, pages={796–805} }
 @article{malvarez_carbone_grunwald_subbarao_schafer_kohn_2007, title={New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington}, volume={97}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-97-4-0470}, abstractNote={ Four populations of Sclerotinia sclerotiorum in North America were inferred previously, based on analyses of both rapidly evolving markers (DNA fingerprint and mycelial compatiblity), and multilocus DNA sequence spanning the range between fast and slow evolution. Each population was defined as an interbreeding unit of conspecific individuals sharing a common recent ancestor and arising in a unique evolutionary event. The present study applies this standard to extend characterization of S. sclerotiorum populations to the Western United States. Isolates of S. sclerotiorum (N = 294) were determined to represent three genetically differentiated populations: California (CA, lettuce), Washington (WA, pea/lentil), and Ontario (ON, lettuce). CA was the most diverse population yet sampled in North America. Clonality was detected in ON and WA. No DNA fingerprints were common among the populations. The index of association (IA), based on fingerprint, was closer to zero (0) for CA than it was for the other populations. High diversity and lack of association of markers in California are consistent either with genetic exchange and recombination, or with large population size and high standing genetic variation. Intra- and interlocus conflict among three DNA sequence loci was consistent with recombination. The coalescent IGS genealogy confirmed subdivision and showed CA to be older than WA or ON. The Nearest Neighbor statistic on combined data confirmed subdivision among all present and previously defined populations. All isolates had both MAT1-1 and MAT1-2, consistent with uniform homothallism. }, number={4}, journal={PHYTOPATHOLOGY}, author={Malvarez, Gabriela and Carbone, Ignazio and Grunwald, Niklaus J. and Subbarao, Krishnamurthy V. and Schafer, Michelle and Kohn, Linda M.}, year={2007}, month={Apr}, pages={470–483} }
 @article{carbone_jakobek_ramirez-prado_horn_2007, title={Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus}, volume={16}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2007.03464.x}, abstractNote={Abstract}, number={20}, journal={MOLECULAR ECOLOGY}, author={Carbone, Ignazio and Jakobek, Judy L. and Ramirez-Prado, Jorge H. and Horn, Bruce W.}, year={2007}, month={Oct}, pages={4401–4417} }
 @article{deng_carbone_dean_2007, title={The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes}, volume={7}, ISSN={["1471-2148"]}, DOI={10.1186/1471-2148-7-30}, abstractNote={Abstract}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Deng, Jixin and Carbone, Ignazio and Dean, Ralph A.}, year={2007}, month={Feb} }
 @article{aylor_price_carbone_2006, title={SNAP: Combine and Map modules for multilocus population genetic analysis}, volume={22}, DOI={10.1093/bioinformatics/bt/136}, number={11}, journal={Bioinformatics}, author={Aylor, D. L. and Price, E. W. and Carbone, Ignazio}, year={2006}, pages={1399–1401} }
 @article{charles_carbone_davies_bird_burke_kerry_opperman_2005, title={Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci}, volume={187}, ISSN={["1098-5530"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-23644445501&partnerID=MN8TOARS}, DOI={10.1128/JB.187.16.5700-5708.2005}, abstractNote={ABSTRACT}, number={16}, journal={JOURNAL OF BACTERIOLOGY}, author={Charles, L and Carbone, I and Davies, KG and Bird, D and Burke, M and Kerry, BR and Opperman, CH}, year={2005}, month={Aug}, pages={5700–5708} }
 @article{price_carbone_2005, title={SNAP: workbench management tool for evolutionary population genetic analysis}, volume={21}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/bti003}, abstractNote={Abstract}, number={3}, journal={BIOINFORMATICS}, author={Price, EW and Carbone, I}, year={2005}, month={Feb}, pages={402–404} }
 @article{dean_talbot_ebbole_farman_mitchell_orbach_thon_kulkarni_xu_pan_et al._2005, title={The genome sequence of the rice blast fungus Magnaporthe grisea}, volume={434}, ISSN={["1476-4687"]}, DOI={10.1038/nature03449}, abstractNote={Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.}, number={7036}, journal={NATURE}, author={Dean, RA and Talbot, NJ and Ebbole, DJ and Farman, ML and Mitchell, TK and Orbach, MJ and Thon, M and Kulkarni, R and Xu, JR and Pan, HQ and et al.}, year={2005}, month={Apr}, pages={980–986} }
 @inbook{carbone_kohn_2004, title={Inferring Process from Pattern in Fungal Population Genetics}, ISBN={9780444516428}, ISSN={1874-5334}, url={http://dx.doi.org/10.1016/s1874-5334(04)80005-4}, DOI={10.1016/s1874-5334(04)80005-4}, abstractNote={The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp. G, and C. zebrina were also identified in association with CLS on B. vulgaris. Cercospora apii and C. cf. flagellaris were pathogenic to table beet but Cercospora sp. G and C. zebrina did not cause disease. Genealogical concordance phylogenetic species recognition, GMYC and PTP methods failed to differentiate C. apii and C. beticola as separate species. On the other hand, multi-species coalescent analysis based on BFD supported separation of C. apii and C. beticola into distinct species; and provided evidence of evolutionary independent lineages within C. beticola. Extensive intra- and intergenic recombination, incomplete lineage sorting and dominance of clonal reproduction complicate evolutionary species recognition in the genus Cercospora. The results warrant morphological and phylogenetic studies to disentangle cryptic speciation within C. beticola.}, booktitle={Fungal Genomics}, publisher={Elsevier}, author={Carbone, Ignazio and Kohn, Linda}, year={2004}, pages={29–58} }
 @article{carbone_liu_hillman_milgroom_2004, title={Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent}, volume={166}, ISSN={["0016-6731"]}, DOI={10.1534/genetics.166.4.1611}, abstractNote={Genealogy-based methods were used to estimate migration of the fungal virus Cryphonectria hypovirus 1 between vegetative compatibility types of the host fungus, Cryphonectria parasitica, as a means of estimating horizontal transmission within two host populations. Vegetative incompatibility is a self/non-self recognition system that inhibits virus transmission under laboratory conditions but its effect on transmission in nature has not been clearly demonstrated. Recombination within and among different loci in the virus genome restricted the genealogical analyses to haplotypes with common mutation and recombinational histories. The existence of recombination necessitated that we also use genealogical approaches that can take advantage of both the mutation and recombinational histories of the sample. Virus migration between populations was significantly restricted. In contrast, estimates of migration between vegetative compatibility types were relatively high within populations despite previous evidence that transmission in the laboratory was restricted. The discordance between laboratory estimates and migration estimates from natural populations highlights the challenges in estimating pathogen transmission rates. Genealogical analyses inferred migration patterns throughout the entire coalescent history of one viral region in natural populations and not just recent patterns of migration or laboratory transmission. This application of genealogical analyses provides markedly stronger inferences on overall transmission rates than laboratory estimates do.}, number={4}, journal={GENETICS}, author={Carbone, I and Liu, YC and Hillman, BI and Milgroom, MG}, year={2004}, month={Apr}, pages={1611–1629} }
 @article{phillips_carbone_gold_kohn_2002, title={Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum}, volume={92}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/phyto.2002.92.7.785}, DOI={10.1094/phyto.2002.92.7.785}, abstractNote={ Both typical late season stem infections and atypical early season rosette infections of canola, a relatively new crop in the southeastern United States, were caused by Sclerotinia sclerotiorum. The 51 DNA fingerprints (from 71 isolates) did not match any fingerprints from previous studies of canola or other crops. Single locus haplotypes from nuclear DNA sequences included 18 in the intergenic spacer (IGS) of the rRNA repeat, four in 44.11, six in translation elongation factor 1α, three in calmodulin (CAL), and two in chitin synthase 1. Contingency permutation testing for associations of infection type with DNA fingerprint, single- or multilocus haplotype, or hierarchically nested clades based on single locus haplotypes found significant association of haplotype with mycelial compatibility group and DNA fingerprint for all loci except CAL. Significant association of IGS haplotypes with symptom type was detected in one pathogen population. Southeastern U.S. canola was infected by both recently evolved, geographically dispersed pathogen genotypes and older, indigenous genotypes (Carbone and Kohn, 2001. Mol. Ecol. 10:947–964). Indigenous haplotypes are infection-type generalists, and the most frequently isolated from rosette infections. In contrast, haplotypes from the most recently evolved, dispersed population were associated one-to-one with infection type, with only the most recently evolved haplotypes infecting rosettes. }, number={7}, journal={Phytopathology}, publisher={Scientific Societies}, author={Phillips, D. V. and Carbone, I. and Gold, S. E. and Kohn, L. M.}, year={2002}, month={Jul}, pages={785–793} }
 @article{carbone_kohn_2001, title={A microbial population-species interface: nested cladistic and coalescent inference with multilocus data}, volume={10}, ISSN={0962-1083 1365-294X}, url={http://dx.doi.org/10.1046/j.1365-294x.2001.01244.x}, DOI={10.1046/j.1365-294x.2001.01244.x}, abstractNote={Abstract}, number={4}, journal={Molecular Ecology}, publisher={Wiley}, author={Carbone, I. and Kohn, L. M.}, year={2001}, month={Apr}, pages={947–964} }
 @article{carbone_kohn_2001, title={Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation}, volume={10}, ISSN={0962-1083 1365-294X}, url={http://dx.doi.org/10.1046/j.0962-1083.2001.01380.x}, DOI={10.1046/j.0962-1083.2001.01380.x}, abstractNote={Abstract}, number={10}, journal={Molecular Ecology}, publisher={Wiley}, author={Carbone, Ignazio and Kohn, Linda M.}, year={2001}, month={Dec}, pages={2409–2422} }
 @article{carbone_kohn_1999, title={A Method for Designing Primer Sets for Speciation Studies in Filamentous Ascomycetes}, volume={91}, ISSN={0027-5514}, url={http://dx.doi.org/10.2307/3761358}, DOI={10.2307/3761358}, abstractNote={A simple method is described for designing primer sets that can amplify specific protein-encoding sequences in a wide variety of filamentous ascomycetes. Using this technique, we successfully desig...}, number={3}, journal={Mycologia}, publisher={JSTOR}, author={Carbone, Ignazio and Kohn, Linda M.}, year={1999}, month={May}, pages={553} }
 @article{carbone_anderson_kohn_1999, title={Patterns of Descent in Clonal Lineages and Their Multilocus Fingerprints Are Resolved with Combined Gene Genealogies}, volume={53}, ISSN={0014-3820}, url={http://dx.doi.org/10.2307/2640916}, DOI={10.2307/2640916}, number={1}, journal={Evolution}, publisher={JSTOR}, author={Carbone, Ignazio and Anderson, James B. and Kohn, Linda M.}, year={1999}, month={Feb}, pages={11} }
 @article{carbone_anderson_kohn_1995, title={A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum}, volume={27}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/bf00313431}, DOI={10.1007/bf00313431}, abstractNote={A 1,380-bp intervening sequence within the mitochondrial small subunit ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum has been sequenced and identified as a group-I intron. This is the first report of an intron in the mt SSU rRNA gene. The intron shows close similarity in secondary structure to the subgroup-IC2 introns from Podospora (ND3i1, ND5i2, and COIi5) and Neurospora (ND5i1). The intron has an open reading frame (ORF) that encodes a putative protein of 420 amino acids which contains two copies of the LAGLI-DADG motif. The ORF belongs to a family of ORFs identified in Podospora (ND3i1, ND4Li1, ND4Li2, ND5i2, and COIi5) and Neurospora (ND5i1). The putative 420-aa polypeptide is also similar to a site-specific endonuclease in the chloroplast large subunit ribosomal RNA (LSU rRNA) gene of the green alga Chlamydomonas eugametos. In each clone of S. sclerotiorum examined, including several clones which were sampled over a 3-year period from geographically separated sites, all isolates either had the intron or lacked the intron within the mt SSU rRNA gene. Screening by means of Southern hybridization and PCR amplification detected the intron in the mt SSU rRNA genes of S. minor, S. trifoliorum and Sclerotium cepivorum, but not in other members of the Sclerotiniaceae, such as Botrytis anamorphs of Botryotinia spp., or in other ascomycetous and basidiomycetous fungi.}, number={2}, journal={Current Genetics}, publisher={Springer Science and Business Media LLC}, author={Carbone, Ignazio and Anderson, James B. and Kohn, Linda M.}, year={1995}, month={Jan}, pages={166–176} }
 @article{carbone_kohn_1993, title={Ribosomal DNA Sequence Divergence within Internal Transcribed Spacer 1 of the Sclerotiniaceae}, volume={85}, ISSN={0027-5514}, url={http://dx.doi.org/10.2307/3760703}, DOI={10.2307/3760703}, abstractNote={Based on morphological and immunological studies, we hypothesize that there are two lineages within the Sclerotiniaceae, a family of plant-infecting ascomycetes in the order Helotiales: 1) genera producing sclerotia, which are tuberlike, melanized masses of hyphae, and 2) genera producing substratal stromata, which are mats of compact hyphae that incorporate plant tissues. We sequenced the Internal Transcribed Spacer (ITS 1), defined by primers ITS 1 and 2, in 43 isolates: 29 sclerotial isolates (19 species in 9 genera), 11 substratal isolates (8 species in 4 genera), and 3 outgroup isolates in the Leotiaceae (3 species in 3 genera). Direct, double-stranded sequencing yielded ca 170 bases for sclerotial isolates and ca 200 bases for substratal and outgroup isolates. MACVECTOR and MULTALIN were used for global alignment, and multiple alignment with hierarchical clustering, respectively. The Internal Transcribed Spacer showed close similarity among most of the sclerotial taxa (76 to 100% similarity to Sclerotinia sclerotiorum). This supports our hypothesis that a sclerotial lineage exists and suggests that this lineage has evolved relatively recently. Isolates of the asexual (mitotic) species Sclerotium cepivorum showed 98% similarity to those of the genus Sclerotinia. Sequence divergence was greater (45 to 65% similarity to S. sclerotiorum) amongst the substratal taxa and our outgroups. Parsimony analysis produced one statistically strongly supported tree for a group of species in the genus Rutstroemia, including Sclerotinia homoeocarpa. Although such subclusters of species can be distinguished using parsimony analysis, we conclude that a substratal lineage cannot be discerned based on sequence data from the ITS. Among these more distantly related taxa, including some substratal ingroup taxa and the outgroup taxa, ITS 1 is saturated with changes and shows relatively equal dissimilarity. The variation observed in the ITS does not resolve among more distantly related taxa.}, number={3}, journal={Mycologia}, publisher={JSTOR}, author={Carbone, Ignazio and Kohn, Linda M.}, year={1993}, month={May}, pages={415} }
 @article{kohn_stasovski_carbone_royer_anderson_1991, title={Mycelial Incompatibility and Molecular Markers Identify Genetic Variability in Field Populations of Sclerotinia sclerotiorum}, volume={81}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/phyto-81-480}, DOI={10.1094/phyto-81-480}, abstractNote={Sixty-three sclerotial strains of Sclerotinia were obtained from transects in two fields of canola (Brassica napus) in Ontario. Mycelial pairings of the strains in all combinations on agar medium produced either an incompatible reaction in which a reaction line between the two strains developed in the interaction zone, or a compatible reaction in which no reaction line developed. The reaction line was a distinct discontinuity between the two strains, visible as a red line on the colony reverse in pairings made on medium amended with red food coloring. Among the 33 strains from the first field, six mycelial compatibility groups (MCGs) were recognized, the largest group including 19 strains (...)}, number={4}, journal={Phytopathology}, publisher={Scientific Societies}, author={Kohn, L.M. and Stasovski, E. and Carbone, I. and Royer, J. and Anderson, J.B.}, year={1991}, pages={480–485} }
 @article{kohn_carbone_anderson_1990, title={Mycelial interactions in Sclerotinia sclerotiorum}, volume={14}, ISSN={0147-5975}, url={http://dx.doi.org/10.1016/0147-5975(90)90023-m}, DOI={10.1016/0147-5975(90)90023-m}, abstractNote={Mycelial interactions were examined among 35 isolates ofSclerotinia sclerotiorum and two Asian species,Sclerotinia asari and an unnamed, Japanese species. Pairings were scored as compatible when strains merged to form one colony and incompatible when strains grew to form two distinct colonies. Incompatible mycelial pairings resulted in an interaction zone in which a distinct reaction line and abundant aerial mycelium or thin mycelium were observed with some variation among replicates. All pairings of a strain with itself were compatible. Of the 31 strains ofS. sclerotiorum tested, 21 were mycelially incompatible with all others. Among the remaining 10 strains ofS. sclerotiorum, there were four mycelial compatibility groups consisting of two or three strains each. Pairings ofS. asari with all other strains resulted in a unique incompatible reaction, a mycelium-free interaction zone. Two of three strains of the Japanese species were intercompatible, but pairings of each of the three strains with all other strains were incompatible. Microscopically, mycelial interactions in pairings of strains were complex. Anastomosis between paired strains was not always observed. This may be due in part to the conversion of many hyphal tips, in both compatible and incompatible interactions, to sites of microconidiogenesis no longer capable of hyphal fusion. Incompatible pairings were followed by hyphal deterioration in one or both strains; hyphal deterioration was not observed in compatible interactions. Of the 31 strains tested, 4 strains ofS. sclerotiorum produced apothecia. Pairings between single ascospore isolates within each strain were compatible, as were pairings with the parent isolate. Mycelial interactions of single ascospore isolates with other strains were identical to those of the parent isolate, indicating that the parent fruitbody was homozygous for any determinant(s) of mycelial incompatibility. The data from this study suggest that a high level of mycelial incompatibility exists among strains ofS. sclerotiorum, comparable to levels of vegetative incompatibility reported in other ascomycetes, that the extent of mycelial incompatibility indicates that genetic heterogeneity exists within the species, and that mycelial compatibility/incompatibility reactions may be an effective way of categorizing intraspecific heterogeneity.}, number={3}, journal={Experimental Mycology}, publisher={Elsevier BV}, author={Kohn, Linda M. and Carbone, Ignazio and Anderson, James B.}, year={1990}, month={Sep}, pages={255–267} }
 @article{edwards_ayroles_stone_carbone_lyman_mackay, title={A transcriptional network associated with natural variation in Drosophila aggressive behavior}, volume={10}, number={7}, journal={Genome Biology}, author={Edwards, A. C. and Ayroles, J. F. and Stone, E. A. and Carbone, M. A. and Lyman, R. F. and Mackay, T. F. C.} }