Ignazio Carbone

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

PLOS ONE.

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

Hoz, C. J., Magain, N., Piatkowski, B., Cornet, L., Dal Forno, M., Carbone, I., … Lutzoni, F. (2023, February 24). SYSTEMATIC BIOLOGY, Vol. 2.

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

PLANT DISEASE, 106(3), 906–917.

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

JOURNAL OF VIROLOGICAL METHODS, 300.

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

PLOS ONE, 17(10).

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, June). DATA IN BRIEF, Vol. 42.

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

FUNGAL BIOLOGY, 126(3), 187–200.

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

Hu, C.-H., Govers, F., Carbone, I., & Ristaino, J. B. (2022, November 5). POTATO RESEARCH, Vol. 11.

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

PHYTOBIOMES JOURNAL, 6(3), 227–235.

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

PLOS COMPUTATIONAL BIOLOGY, 18(8).

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

COMMUNICATIONS BIOLOGY, 4(1).

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

PLANT DISEASE, 105(3), 691–694.

Methodological Approaches Frame Insights into Endophyte Richness and Community Composition

MICROBIAL ECOLOGY, 82(1), 21–34.

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

MOLECULAR ECOLOGY, 30(10), 2404–2416.

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 inAspergillus flavus

MYCOLOGIA, 112(5), 908–920.

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

AGRONOMY JOURNAL, 111(2), 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

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

Molecular Ecology, 27(3), 737–751.

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.

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

Phytopathology, 107(3), 313–321.

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

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

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

PHYTOPATHOLOGY, 107(6), 777–785.

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

PLOS ONE, 11(1).

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

FUNGAL GENETICS AND BIOLOGY, 81, 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

FUNGAL GENETICS AND BIOLOGY, 84, 62–72.

Sexual recombination in Aspergillus tubingensis

MYCOLOGIA, 107(2), 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

[Review of ]. ECOLOGY AND EVOLUTION, 4(22), 4399–4428.

GENETIC VARIATION IN HORIZONTALLY TRANSMITTED FUNGAL ENDOPHYTES OF PINE NEEDLES REVEALS POPULATION STRUCTURE IN CRYPTIC SPECIES

AMERICAN JOURNAL OF BOTANY, 101(8), 1362–1374.

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

Bioinformatics, 30(10), 1488–1490.

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

[Review of ]. WORLD MYCOTOXIN JOURNAL, 7(1), 63–82.

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

ECOLOGY AND EVOLUTION, 4(18), 3642–3661.

Sexual Reproduction in Aspergillus flavus Sclerotia Naturally Produced in Corn

PHYTOPATHOLOGY, 104(1), 75–85.

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

MOLECULAR ECOLOGY RESOURCES, 14(5), 1032–1048.

A calibrated human Y-chromosomal phylogeny based on resequencing

GENOME RESEARCH, 23(2), 388–395.

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

NEW PHYTOLOGIST, 198(2), 525–535.

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 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.

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

MOLECULAR ECOLOGY, 21(6), 1453–1476.

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.

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.

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

PHYTOPATHOLOGY, 101(1), 147–153.

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

TOXIN REVIEWS, 30(2-3), 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 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

MOLECULAR ECOLOGY, 18(6), 1161–1174.

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

PHYTOPATHOLOGY, 99(6), 765–774.

Population Genetic Analysis of an Eastern US Wheat Powdery Mildew Population Reveals Geographic Subdivision and Recent Common Ancestry with UK and Israeli Populations

PHYTOPATHOLOGY, 99(7), 840–849.

Recombination and lineage-specific gene loss in the aflatoxin gene cluster of Aspergillus flavus

MOLECULAR ECOLOGY, 18(23), 4870–4887.

Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus

FUNGAL GENETICS AND BIOLOGY, 46(2), 169–175.

Sexual reproduction in Aspergillus flavus

MYCOLOGIA, 101(3), 423–429.

The sexual state of Aspergillus parasiticus

MYCOLOGIA, 101(2), 275–280.

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

BMC GENOMICS, 9.

Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus

FUNGAL GENETICS AND BIOLOGY, 45(9), 1292–1299.

Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer

CANADIAN JOURNAL OF FOREST RESEARCH, 38(6), 1576–1589.

GT-Miner: a graph-theoretic data miner, viewer, and model processor

Bioinformation, 3(5), 235–237.

Phylogenetic relatedness of the M2 double-stranded RNA in Rhizoctonia fungi

MYCOLOGIA, 100(4), 555–564.

Virulence structure of the Eastern US wheat powdery mildew population

PLANT DISEASE, 92(7), 1074–1082.

An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104(9), 3306–3311.

Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster

BMC EVOLUTIONARY BIOLOGY, 7.

Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancylostoma caninum)

JOURNAL OF PARASITOLOGY, 93(4), 796–805.

New populations of Sclerotinia sclerotiorum from lettuce in California and peas and lentils in Washington

PHYTOPATHOLOGY, 97(4), 470–483.

Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus

MOLECULAR ECOLOGY, 16(20), 4401–4417.

The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes

BMC EVOLUTIONARY BIOLOGY, 7.

SNAP: Combine and Map modules for multilocus population genetic analysis

Bioinformatics, 22(11), 1399–1401.

Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci

JOURNAL OF BACTERIOLOGY, 187(16), 5700–5708.

SNAP: workbench management tool for evolutionary population genetic analysis

BIOINFORMATICS, 21(3), 402–404.

The genome sequence of the rice blast fungus Magnaporthe grisea

NATURE, 434(7036), 980–986.

Inferring Process from Pattern in Fungal Population Genetics

In Fungal Genomics (pp. 29–58).

Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent

GENETICS, 166(4), 1611–1629.

Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum

Phytopathology, 92(7), 785–793.

A microbial population-species interface: nested cladistic and coalescent inference with multilocus data

Molecular Ecology, 10(4), 947–964.

Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation

Molecular Ecology, 10(10), 2409–2422.

A Method for Designing Primer Sets for Speciation Studies in Filamentous Ascomycetes

Mycologia, 91(3), 553.

Patterns of Descent in Clonal Lineages and Their Multilocus Fingerprints Are Resolved with Combined Gene Genealogies

Evolution, 53(1), 11.

A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum

Current Genetics, 27(2), 166–176.

Ribosomal DNA Sequence Divergence within Internal Transcribed Spacer 1 of the Sclerotiniaceae

Mycologia, 85(3), 415.

Mycelial Incompatibility and Molecular Markers Identify Genetic Variability in Field Populations of Sclerotinia sclerotiorum

Phytopathology, 81(4), 480–485.

Mycelial interactions in Sclerotinia sclerotiorum

Experimental Mycology, 14(3), 255–267.

A transcriptional network associated with natural variation in Drosophila aggressive behavior

Edwards, A. C., Ayroles, J. F., Stone, E. A., Carbone, M. A., Lyman, R. F., & Mackay, T. F. C. Genome Biology, 10(7).