Ignazio Carbone

Evolutionary Relationships and a T-BAS Interactive Phylogeny of Emerging Lineages of the Plant Pathogen Phytophthora ramorum

Mainello-Land, A., O'Hanlon, R., Carbone, I., & Ristaino, J. B. (2026, January 7). Phytopathology.

A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species

PLOS ONE, 20(1), e0314509.

An emerging fungal disease is spreading across the globe and affecting the blueberry industry

Bradshaw, M., Ivors, K., Broome, J. C., Carbone, I., Braun, U., Yang, S., … Pfister, D. H. (2025, January 8). New Phytologist, Vol. 1.

Global population genomics redefines domestication and clinical diversity in the Aspergillus flavus–oryzae complex

Pfliegler, W. P., Németh, B., Bodnár, V., Pusztahelyi, T., Carbone, I., & Pócsi, I. (2025, December 23). IMA Fungus, Vol. 12.

Preserving the Biologically Coherent Generic Concept of Phytophthora, “Plant Destroyer”

Preserving the Biologically Coherent Generic Concept of Phytophthora, “Plant Destroyer.” Phytopathology®, 115(6), 573–586.

Rhs-toxin Abundance, Diversity, and Function in Four Genera of Plant Pathogenic Bacteria: Xanthomonas, Ralstonia, Pectobacterium, and Dickeya

Cabrera, A. G., Ameen, Y. O., Katherine, D. A.-W., Joglekar, P., Huguet-Tapia, J., Carbone, I., & Huerta, A. I. (2025, May 13). (Vol. 5). Vol. 5.

Eco‐phylogenetic study of Trebouxia in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont

Medeiros, I. D., Ibáñez, A., Arnold, A. E., Hedderson, T. A., Miadlikowska, J., Flakus, A., … Lutzoni, F. (2024, December 1). American Journal of Botany, Vol. 12.

Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth’s largest terrestrial biome

U’Ren, J. M., Oita, S., Lutzoni, F., Miadlikowska, J., Ball, B., Carbone, I., … Arnold, A. E. (2024, February 16). Current Biology, Vol. 34.

An open-access T-BAS phylogeny for emerging Phytophthora species

Coomber, A., Saville, A., Carbone, I., & Ristaino, J. B. (2023, April 3). (J. E. Blair, Ed.). PLoS ONE, Vol. 18.

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Hoz, C. J. P.-D., Magain, N., Piatkowski, B., Cornet, L., Forno, M. D., Carbone, I., … Lutzoni, F. (2023, February 24). (C. Lemus-Solis, Ed.). Systematic Biology, Vol. 2.

Cassava begomovirus species diversity changes during plant vegetative cycles

Frontiers in Microbiology, 14.

Towards a nomenclatural clarification of the Peltigera ponojensis/monticola clade including metagenomic sequencing of type material and the introduction of P. globulata Miadl. & Magain sp. nov.

Miadlikowska, J., Magain, N., Medeiros, I. D., Hoz, C. J. P.-D., Carbone, I., LaGreca, S., … Lutzoni, F. (2023, September 1). The Lichenologist, Vol. 55, pp. 315–324.

Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control

Molo, M. S., White, J. B., Cornish, V., Gell, R. M., Baars, O., Singh, R., … Carbone, I. (2022, October 27). (W. C. Nierman, Ed.). PLoS ONE, Vol. 17.

Dataset for transcriptomic profiles associated with development of sexual structures in Aspergillus flavus

Luis, J. M., Carbone, I., Mack, B. M., Lebar, M. D., Cary, J. W., Gilbert, M. K., … Ojiambo, P. S. (2022, March 14). Data in Brief, Vol. 6.

Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus

Luis, J. M., Carbone, I., Mack, B. M., Lebar, M. D., Cary, J. W., Gilbert, M. K., … Ojiambo, P. S. (2022, January 31). Fungal Biology, Vol. 3.

Gene Flow of Phytophthora infestans Between Refuse Piles, and Organic and Conventional Potato Fields in Southern Flevoland, The Netherlands

Potato Research, 66(3), 701–721.

Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage

Ahmad, J., Zervas, A., Ellegaard-Jensen, L., Hennessy, R. C., Carbone, I., Cornish, V., … Nicolaisen, M. H. (2022, October 6). Microbiology Resource Announcements, Vol. 10.

Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana

Hoyer, J. S., Wilkins, O. W., Munshi, A., Wiese, E., Dubey, D., Renard, S., … Ascencio-Ibáñez, J. T. (2022, March 14). Phytobiomes Journal, Vol. 6, pp. 227–235.

Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination

PLOS Computational Biology, 18(8), e1010422.

Adaptation of Phytophthora nicotianae to Multiple Sources of Partial Resistance in Tobacco

Jin, J., McCorkle, K. L., Cornish, V., Carbone, I., Lewis, R. S., & Shew, H. D. (2021, November 4). Plant Disease, Vol. 106, pp. 906–917.

An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing

Aimone, C. D., Hoyer, J. S., Dye, A. E., Deppong, D. O., Duffy, S., Carbone, I., & Hanley-Bowdoin, L. (2021, December 9). Journal of Virological Methods, Vol. 2, p. 114405.

Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale

Oita, S., Ibáñez, A., Lutzoni, F., Miadlikowska, J., Geml, J., Lewis, L. A., … Arnold, A. E. (2021, March 9). Communications Biology, Vol. 4.

Methodological Approaches Frame Insights into Endophyte Richness and Community Composition

Oita, S., Carey, J., Kline, I., Ibáñez, A., Yang, N., Hom, E. F. Y., … Arnold, A. E. (2021, January 7). Microbial Ecology.

Parasites, niche modification and the host microbiome: A field survey of multiple parasites

O’Keeffe, K. R., Halliday, F. W., Jones, C. D., Carbone, I., & Mitchell, C. E. (2021, March 19). Molecular Ecology.

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

Journal of General Virology, 102(7).

Characterization of morphological changes within stromata during sexual reproduction in Aspergillus flavus

Luis, J. M., Carbone, I., Payne, G. A., Bhatnagar, D., Cary, J. W., Moore, G. G., … Ojiambo, P. S. (2020, August 21). Mycologia.

Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana

Crouch, J. A., Beirn, L. A., Boehm, M. J., Carbone, I., Clarke, B. B., Kerns, J. P., … Tredway, L. P. (2020, July 21). Plant Disease, Vol. 105, pp. 691–694.

A Response to the Letter to the Editor from Ortega-Beltran and Bandyopadhyay

Agronomy Journal, 111(5), 2629–2631.

Biocontrol Strains Differentially Shift the Genetic Structure of Indigenous Soil Populations of Aspergillus flavus

Frontiers in Microbiology, 10.

HPLC quantitation of aflatoxin B1 from fungal mycelium culture

Journal of Microbiological Methods, 158, 14–17.

Host availability drives distributions of fungal endophytes in the imperilled boreal realm

Nature Ecology & Evolution, 3(10), 1430–1437.

Identification and characterization of Septoria steviae as the causal agent of Septoria leaf spot disease of stevia in North Carolina

Mycologia, 111(3), 456–465.

Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States

PLOS ONE, 14(3), e0214214.

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

Microbiology Resource Announcements, 8(29).

Trial Summary on the Comparison of Various Non‐Aflatoxigenic Strains of Aspergillus flavus on Mycotoxin Levels and Yield in Maize

Molo, M. S., Heiniger, R. W., Boerema, L., & Carbone, I. (2019, January 24). Agronomy Journal, Vol. 111, pp. 942–946.

Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass

Fungal Biology, 122(8), 761–773.

Cultural and Genetic Approaches to Manage Aflatoxin Contamination: Recent Insights Provide Opportunities for Improved Control

Phytopathology, 108(9), 1024–1037.

Management practices for controlling mycotoxins in corn: A three-year summary

(NC State Extension Publications No. AG-852). http://content.ces.ncsu.edu/management-practices-for-controlling-mycotoxins-in-corn

Balancing selection for aflatoxin in Aspergillus flavus is maintained through interference competition with, and fungivory by insects

Proceedings of the Royal Society B: Biological Sciences, 284(1869), 20172408.

Global population structure and adaptive evolution of aflatoxin-producing fungi

Ecology and Evolution, 7(21), 9179–9191.

Plastic potential: how the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants

Current Opinion in Plant Biology, 38, 78–83.

Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe

Population structure and migration of the Tobacco Blue Mold Pathogen,Peronospora tabacina,into North America and Europe. Molecular Ecology, 27(3), 737–751.

Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of Pseudoperonospora cubensis

Ecology and Evolution, 7(16), 6231–6246.

Virulence Structure Within Populations of Pseudoperonospora cubensis in the United States

Thomas, A., Carbone, I., Lebeda, A., & Ojiambo, P. S. (2017, February 14). Phytopathology, Vol. 107, pp. 777–785.

Occurrence and Distribution of Mating Types of Pseudoperonospora cubensis in the United States

Phytopathology, 107(3), 313–321.

Sexual Reproduction in Aspergillus flavus Sclerotia: Acquisition of Novel Alleles from Soil Populations and Uniparental Mitochondrial Inheritance

Horn, B. W., Gell, R. M., Singh, R., Sorensen, R. B., & Carbone, I. (2016, January 5). PLoS ONE, Vol. 11.

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life

Bioinformatics, 33(8), btw808.

Characterization and distribution of mating-type genes of the turfgrass pathogen Sclerotinia homoeocarpa on a global scale

Putman, A. I., Tredway, L. P., & Carbone, I. (2015, June 6). Fungal Genetics and Biology, Vol. 81, pp. 25–40.

Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus

Molecular Ecology, 24(8), 1889–1909.

Genetic structure and post-glacial expansion ofCornus floridaL. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling

Journal of Systematics and Evolution, 54(2), 136–151.

Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species

Current Genetics, 61(4), 567–577.

Nuclear heterogeneity in conidial populations of Aspergillus flavus

Runa, F., Carbone, I., Bhatnagar, D., & Payne, G. A. (2015, September 8). Fungal Genetics and Biology, Vol. 84, pp. 62–72.

Sexual recombination in Aspergillus tubingensis

Olarte, R. A., Horn, B. W., Singh, R., & Carbone, I. (2015, March 1). Mycologia, Vol. 107, pp. 307–312.

The Use of Management Practices to Reduce Mycotoxin Contamination in Corn

(NC State Extension Publication No. AG-807). Raleigh, NC: North Carolina Cooperative Extension Service.

Challenges in analysis and interpretation of microsatellite data for population genetic studies

Putman, A. I., & Carbone, I. (2014, October 30). Ecology and Evolution, Vol. 4, pp. 4399–4428.

Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species

Oono, R., Lutzoni, F., Arnold, A. E., Kaye, L., U’Ren, J. M., May, G., & Carbone, I. (2014, August 1). American Journal of Botany, Vol. 101, pp. 1362–1374.

Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics

Bioinformatics, 30(10), 1488–1490.

Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity

Barnes, I., Wingfield, M. J., Carbone, I., Kirisits, T., & Wingfield, B. D. (2014, September 1). Ecology and Evolution, Vol. 4, pp. 3642–3661.

Tissue storage and primer selection influence pyrosequencing‐based inferences of diversity and community composition of endolichenic and endophytic fungi

U'Ren, J. M., Riddle, J. M., Monacell, J. T., Carbone, I., Miadlikowska, J., & Arnold, A. E. (2014, March 15). Molecular Ecology Resources, Vol. 14, pp. 1032–1048.

Development and characterization of 14 microsatellite loci for the plant pathogenic fungus Sclerotinia homoeocarpa

Molecular Ecology Resources, 13(5), 966–968.

Fragmentation of an aflatoxin‐like gene cluster in a forest pathogen

Bradshaw, R. E., Slot, J. C., Moore, G. G., Chettri, P., Wit, P. J. G. M., Ehrlich, K. C., … Cox, M. P. (2013, March 1). New Phytologist, Vol. 198, pp. 525–535.

Mycotoxins that affect the North American agri-food sector: state of the art and directions for the future

Miller, J. D., Schaafsma, A. W., Bhatnagar, D., Bondy, G., Carbone, I., Harris, L. J., … Zhou, T. (2013, December 10). World Mycotoxin Journal, Vol. 7, pp. 63–82.

Permanent genetic resources added to molecular ecology resources database 1 April 2013-31 May 2013

Molecular Ecology Resources, 13(5), 966–968.

Sexual Reproduction in Aspergillus flavus Sclerotia Naturally Produced in Corn

Horn, B. W., Sorensen, R. B., Lamb, M. C., Sobolev, V. S., Olarte, R. A., Worthington, C. J., & Carbone, I. (2013, July 24). Phytopathology, Vol. 104, pp. 75–85.

Sexual reproduction in Aspergillus tubingensis from section Nigri

Mycologia, 105(5), 1153–1163.

Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

PLoS Pathogens, 9(8), e1003574.

A calibrated human Y-chromosomal phylogeny based on resequencing

Wei, W., Ayub, Q., Chen, Y., McCarthy, S., Hou, Y., Carbone, I., … Tyler-Smith, C. (2012, October 4). Genome Research, Vol. 23, pp. 388–395.

Renaming the dollar spot fungus

Golf Course Management Current Research.

A multidimensional study of endophytic fungal diversity

IMA Fungus, 2(1), 2–4.

Climate change impacts on mycotoxin risks in US maize

World Mycotoxin Journal, 4(1), 79–93.

Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis

OLARTE, R. O. D. R. I. G. O. A., HORN, B. R. U. C. E. W., DORNER, J. O. E. W., MONACELL, J. A. M. E. S. T., SINGH, R. A. K. H. I., STONE, E. R. I. C. A., & CARBONE, I. G. N. A. Z. I. O. (2011, December 29). Molecular Ecology, Vol. 21, pp. 1453–1476.

Evidence that the Human Pathogenic Fungus Cryptococcus neoformans var. grubii May Have Evolved in Africa

PLoS ONE, 6(5), e19688.

Phylogenetic history of Phytophthora cryptogea and P. drechsleri Isolates from floriculture crops in North Carolina greenhouses

Phytopathology, 101(11), 1373–1384.

Selection of Aspergillus flavus isolates for biological control of aflatoxins in corn

Abbas, H. K., Weaver, M. A., Horn, B. W., Carbone, I., Monacell, J. T., & Shier, W. T. (2011, July 19). Toxin Reviews, Vol. 30, pp. 59–70.

Sexual reproduction in aflatoxin-producing Aspergillus nomius

Mycologia, 103(1), 174–183.

The Population Dynamics of Aflatoxigenic Aspergilli

In R. G. Guevara-González (Ed.), Aflatoxins - Biochemistry and Molecular Biology.

Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia

Kaye, A. C., Moyer, J. W., Parks, E. J., Carbone, I., & Cubeta, M. A. (2010, September 14). Phytopathology, Vol. 101, pp. 147–153.

Population genetic analysis reveals ancient evolution and recent migration of P. ramorum

[Tech. Rep. PSW-GTR-229.]. In S. J. Frankel, J. T. Kliejunas, & K. M. Palmieri (Eds.), Proceedings of the Sudden Oak Death Fourth Science Symposium (pp. 116–118).

Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum

GOSS, E. M., CARBONE, I., & GRÜNWALD, N. J. (2009, February 16). Molecular Ecology, Vol. 18, pp. 1161–1174.

Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches

Lourenço, V., Moya, A., González-Candelas, F., Carbone, I., Maffia, L. A., & Mizubuti, E. S. G. (2009, May 19). Phytopathology, Vol. 99, pp. 765–774.

Population Genetic Analysis of an Eastern U.S. Wheat Powdery Mildew Population Reveals Geographic Subdivision and Recent Common Ancestry with U.K. and Israeli Populations

Parks, R., Carbone, I., Murphy, J. P., & Cowger, C. (2009, June 12). Phytopathology, Vol. 99, pp. 840–849.