INTEGRATED RESOURCES SUPPORTING INQUIRIES ABOUT THE EVOLUTION, PATHOLOGY AND ECOLOGY OF FUSARIUM TOWARDS THE GOAL OF ENSURING FOOD SECURITY AND SAFETY

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1016291
• Project Start Date: Jul 1, 2018
• Project End Date: Jun 30, 2023
• Program Code: [(N/A)]- (N/A)

Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802

Performing Department
Plant Pathology & Environmental Microbiology

Non Technical Summary
In the coming decades, population growth and rising consumption per capita around the world will steadilyincrease the amount of additional food, feed and fiber needed. Meeting this need faces a number of complexchallenges, one of which is how to minimize crop loss caused by diverse pathogenic and toxigenicmicroorganisms without continuous heavy reliance on synthetic pesticides. Through this project, we will generatedata and tools that will help effectively manage one of the most threatening groups of fungi, Fusarium. Plantpathogenic Fusarium species threaten practically every major food and ornamental crop around the world, as wellas many plants of environmental significance. Some species also produce several types of metabolites that arehighly toxic to animals and plants. Using accumulated resources and expertise on Fusarium at Penn State, we willgenerate data and tools that will support the following: (a) accurate identification of Fusarium species; (b)research on their biology, ecology, and pathology; and (c) application of accumulated knowledge to solve variousproblems.

Animal Health Component

40%

Research Effort Categories

Basic

60%

Applied

40%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
212	0199	1102	50%
212	0199	1070	25%
212	0199	1040	25%

Knowledge Area
212 - Pathogens and Nematodes Affecting Plants;

Subject Of Investigation
0199 - Soil and land, general;

Field Of Science
1040 - Molecular biology; 1070 - Ecology; 1102 - Mycology;

Keywords

diagnosis

food safety

fusarium

fungal ecology

mycotoxins

pathogen identification

Goals / Objectives
Goals and SignificanceFew fungal genera can claim the multifaceted notoriety of Fusarium as a threat to global food security and safety.The genus comprises at least ~300 known phylogenetic species, many of which are morphologically cryptic, andonly about half of which have been formally described. Plant pathogenic species threaten practically every majorfood and ornamental crop around the world, as well as many plants of environmental significance. Some speciesproduce several types of secondary metabolites (SMs) that are highly toxic to animals and plants (Brown andProctor, 2016). Although Fusarium is best known for such pathogenic or toxigenic species, the genus alsoincludes phylogenetically diverse endophytes, soil and aquatic biofilm saprophytes, human pathogens and evennutritional symbionts of insects. Because of its ecological ubiquity, diverse life styles, and worldwide impact asan agent of plant and human diseases and producer of toxic SMs, countless stakeholders seek information relatedto Fusarium diversity, biology, evolution, pathology or ecology.Penn State has been a world leader for decades in generating and disseminating such information, in large partdue to Fusarium Research Center (FRC) housed at Penn State. FRC archives the world's largest collection ofFusarium isolates from diverse regions and substrates. This culture collection and in house expertise havesupported a wide range of fundamental research on Fusarium and practical problem solving. With the availabilityof genome sequences that cover the spectrum of phylogenetic, pathogenic and mycotoxigenic diversity within thegenus, we can holistically explore the genetic basis of their biology, ecology, pathology, and evolution. Thisproposal builds on this opportunity and will focus on generating data and tools that will support the identification,discovery and description of Fusarium species as well as enhancing the mechanistic understanding of howFusarium interacts with other organisms.Specific ObjectivesSupport the characterization of novel and emerging Fusarium pathogens and toxin producersthrough the following activities:a. Establish robust and comprehensive molecular phylogeny of the genus Fusarium usingadditional, phylogenetically informative loci identified via comparative genomics (Geiser, Kang, and Jimenez-Gasco);b. Better resolve phylogenetic relationships among agriculturally important Species Complexes (Geiser).Generate the following diagnostic resources to help frontline researchers in agriculture and otherfields:a. Improved online platforms with more sequence data and more isolates and useful informationassociated with characterized isolates/identification results (Geiser and Kang);b. Electronic and printed publications summarizing Fusarium taxonomy and important SpeciesComplexes (Geiser);Explore the genetic and chemical basis of Fusarium ecology in association with plants and othermicrobes with a focus on the following questions:a. Which secreted metabolites function as signals to plants and/or other microbes? (Kang);b. How do such metabolites affect plants and/or other microbes? (Kang)

Project Methods
1. Objective 1: New genome sequence-based methods will be used to identify orthologous genes from a set of complete genome sequences. Primers that are ortholog-specific are designed corresponding to sites within genes that are conserved across the taxon of interest, usually located in exon regions that flank introns that are informative at the species level. Phylogenetic relationships are inferred using a consensus approach, utilizing maximum parsimony, Bayesian and Maximum Likelihood methods. Bootstrap as well as Bayesian posterior probabilities are used as indicators of node support. Intraspecific polymorphism identified in these markers can be used for population analyses, as well as nucleotide polymorphism identified in other loci (especially intergenic regions), and tandem repeats (i.e., microsatellites). Species boundaries are inferred using principles of genealogical concordance. Resulting sequence data, along with any available phenotypic traits of each species and individual isolates within species (such as morphology, growth characteristics, profiles of secondary metabolites) will be archived (Objective 2). These databases will support pathogen identification and risk assessment of newly isolated strains. While multiple loci are generally required to infer robust phylogenies and to recognize species boundaries, a single locus can be implemented as a quick identification tool. A ~700 bp portion of the 5' end of the translation elongation factor 1-alpha gene has proven to be a very powerful tool for identifying Fusarium isolates to phylogenetically defined species. In recent years, we have added full DNA sequences of the largest and second largest B-subunits of the RNA Polymerase II genes, which despite lacking introns are highly informative even at the species level. Sequence based identification of unknown pathogens using these loci involves DNA sequencing of the target locus, followed by BLAST searches to identify best hits against a database of sequences corresponding to vouchered, publicly available specimens.2. Objective 2: We will unify FUSARIUM-ID and Fusarium-MLST under a single tool housed at CBS. The original sequence content in FUSARIUM-ID was cobbled together from many independent alignment files generated by the project participants, so annotations are inconsistent, and updates are extremely cumbersome. The first task will be to refine the current annotations of all sequences in FUSARIUM-ID, so they have consistent sequence identifiers that provide the isolate name, locus name, and phylogenetic species identification, using best practices for annotation and wherever possible providing minimal information standards. In addition, sequences from several published studies have yet to be added to the database. Once a defined identifier format for sequences that connects them to isolates and taxa is in place, it will be possible to do subsequent updates in bulk, and with great ease. Importantly, sequence annotations in FUSARIUM-ID will provide links back to the nomenclatural database MycoBank, managed by collaborators Crous and Robert, so that users will find summaries of nomenclature and other relevant information and data. In print form, the monograph will consist of several introductory chapters, followed by taxonomy chapters (Species Complexes and Species) organized phylogenetically. In the electronic form, Species Complex and species names will be hyperlinked for cross-referencing. On each Species Complex page, a list of links to component species will appear, and on a species page, there will be a link back to its corresponding Species Complex page. Also, each species page will contain a link to a list of isolates for which there are data in FUSARIUM-ID. Clicking on any one isolate will provide a link to a page showing the basic annotation information for that isolate (culture collection, accession number, accession number in other collections, substrate of origin, and geographic origin) as well as links to each sequence associated with that isolate. Conversely, query results in FUSARIUM-ID will produce hyperlinked results: species names in a BLAST result will link back to the species page in the monograph.3. Objective 3: Employment of diverse metabolites by plants to regulate key processes, such as defense, communication with other organisms, growth and development, likely presented evolutionary opportunities for microbes to hijack or manipulate such processes for their advantage by releasing the same metabolites or their structural or functional analogs. Similarly, metabolite-mediated interactions among microbes affect the structure and function of the microbiomes associated with diverse organisms and environments. The involvement of secreted metabolites in diverse organismal interactions underscores the importance of understanding the nature and mechanism of this mode of interaction to understand microbial ecology and evolution. However, compared to research on secreted proteins, research on secreted metabolites lags considerably behind. Based on our published and preliminary data suggesting the involvement of certain secreted metabolites, including some that are volatile, in Fusarium interaction with plants and other fungi, we will employ molecular genetic, analytical, genomics tools (e.g., gene manipulation, metabolomics, transcriptomics) to characterize the nature, roles and mechanisms of action of such metabolites.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Fundamental and applied researchers, clinicians and stakeholders in industry, government and academic institutions studying plant diseases, mycotoxins and fungal genomics and evolution. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Geiser PhD student, Emma Wallace, continuously mentored Chyanna McGee, a minority MS student, in performing Fusarium laboratory and field research. PhD students Wallace and Terry Torres-Cruz developed videos and other materials for a two-day Fusarium workshop associated with the Latin American Mycological Congress, which will be held remotely due to the COVID-19 epidemic. Two postdocs in Kang lab, Ningxiao Li and Rhea Lumactud, attended a five-day workshop on Microbial Genomics and Metagenomics organized by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). This hands-on workshop taught them how to use the genomic and metagenomic datasets and computational tools in JGIto perform (meta)genome exploration, comparative genomics and gene discovery. Ningxiao Li continuously mentored Amy Kovaleski, an undergraduate student, via an internally supported project that aims to screen and identify secreted fungal metabolites inhibiting the production of aflatoxins, a group of fungal toxins that pose grave health threats around the world. How have the results been disseminated to communities of interest?Besides the papers noted in this report, Kang presented the work on volatile-mediated fungal interactions with plants and other microorganisms atsix universities around Korea. What do you plan to do during the next reporting period to accomplish the goals?Goal 1. Jiménez-Gasco will complete work on the diversity of endophytic populations of Fusarium oxysporum colonizing banana. Goals 1-2: Geiser will lead a publication now in revision for the Fusarium phylogenomic study described in the O'Donnell et al. (2020) paper in mSphere. Geiser's laboratory is completing an additional >50 Fusarium oxysporum genomes, which will be used to develop diagnostic markers based on pathogen-specific sequences. Goals 3-4 Kang will employ a combination of metabolomics, transcriptomics, and targeted gene manipulation to identify specific volatile compounds of F. oxysporum and Trichoderma biocontrol agents affecting plant health and other soil microbes.

Impacts
What was accomplished under these goals? Goals 1b, 2a and 2b: Geiser and collaborators compiled a 19-locus dataset derived from complete genome sequences of 84 Fusarium species, and analyzed them to demonstrate robustly that the genus Fusarium has a single evolutionary origin. These 19 loci are distributed throughout the core Fusarium genome and can be utilized for diagnostic purposes. Goal 1b: Jimenez-Gasco and former PhD student Freddy Magdama evaluated the diversity and biology ofFusarium oxysporum associated to banana in Ecuador. A total of 298 isolates of F. oxysporum were obtained from banana plants displaying symptoms of Fusarium wilt from several provinces in the coastal area of Ecuador, the most important banana-producing areain Ecuador. Populations were studied using phylogenetic analyses based on sequences of partial TEF and IGS regions, VCG and mating type analyses, and pathogenicity testing on Cavendish 'Williams,''Bluggoe' and 'Gros Michel' banana plants in growth chambers. Our results revealed that F. oxysporum f.sp. cubense populations in Ecuador comprise a single clonal lineage, associated with vegetative compatibility groups (VCG) 0120. Isolates belonging to the same VCG0120 have historically caused disease on 'Gros Michel' cultivars in the subtropics. Goals 3a and 3b: Kang and his postdocs have characterized how Trichoderma biocontrol agents respond to five volatile compounds produced by F. oxysporum via RNAseq analysis. This analysis is based on our previous workshowing that volatile compounds produced by F. oxysporum induced the production of antifungal molecules secreted by Trichoderma in a species/strain-dependent manner. Goals 3a and 3b: Kang and his postdocs have investigated how two Trichoderma biocontrol agents interact with rhizosphere bacteria isolated from a tomato plant via secreted proteins, metabolites, and volatile compounds. The secretion of antibacterial and antifungal molecules by T. virens and T. harzianum was significantly affected by volatile compounds from some bacteria, suggesting that both Trichoderma and rhizosphere bacteria use volatile compounds to influence each other in multiple ways.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Li, N., Islam, M., and Kang, S. (2019) Secreted metabolite-mediated interactions between rhizosphere bacteria and Trichoderma biocontrol agents. PLoS One 14: e0227228.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Kellogg, J. and Kang, S. (2020) Metabolomics, an essential tool in exploring and harnessing microbial chemical ecology. Phytobiomes J. 4: 195-210.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Lucking, R., Aime, M.C., Robbertse, B., Miller, A.N., Ariyawansa, H.A., Aoki, T., Cardinali, G., Crous, P.W., Druzhinina, I.S., Geiser, D.M., Hawksworth, D.L., Hyde, K.D., Irinyi, L., Jeewon, R., Johnston, P.R., Kirk, P.M., Malosso, E., May, T.W., Meyer, W., Opik, M., Robert, V. Stadler, M., Thines, M., Vu, D., Yurkov, A.M., Zhang, N., and Schoch, C.L.. (2020) Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11: 14.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: O'Donnell, K., Al-Hatmi, A.M.S., Aoki, T., Brankovics, B., Cano-Lira, J.F., Coleman, J.J., de Hoog, G.S., Di Pietro, A., Frandsen, R.J.N., Geiser, D.M., Gibas, C.F.C., Guarro, J., Kim, H-S., Kistler, H.C., Laraba, I., Leslie, J.F., Lopez-Berges, M.S., Lysoe, E., Meis, J.F., Monod, M., Proctor, R.H., Rep, M., Ruiz-Roldan, C., Sisic, A., Stajich, J.E., Steenkamp, E.T., Summerell, B.A., van der Lee, T.A.J., van Diepeningen, A.D., Verweij, P.E., Waalwijk, C., Ward, T.J., Wickes, B.L., Wiederhold, N.P., Wingfield, M.J., Zhang, N., Zhang, S.X. (2020) No to Neocosmospora: Phylogenomic and practical reasons for continued inclusion of the Fusarium solani Species Complex in the genus Fusarium. mSphere 5: e00810-20.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Magdama, F., Monserrate-Maggi, L., Serrano, L., Garcia-Onofre, J., and Jim�nez-Gasco, M. M. 2020. Genetic diversity of Fusarium oxysporum f. sp. cubense, the Fusarium wilt pathogen of banana, in Ecuador. Plants, 9: 1133.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Crandall, S. G., Gold, K. M., Jimenez-Gasco, M. M., Filgueiras, C. C., and Willett, D. S. A multi-omics approach to solving problems in plant disease ecology. 2020. PLoS ONE, 15(9): e0237975.

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Fundamental and applied researchers, clinicians and stakeholders in industry, government and academic institutions studying plant diseases, mycotoxins and fungal genomics and evolution. We seek taxonomic clarity in Fusarium that will assist efforts to detect, monitor and manage Fusarium disease and toxin issues. We seek improved understanding of the ecological, molecular and genomic underpinnings of the evolution and emergence of new Fusarium pathogens and diseases, with the goal of facilitating the discovery of novel disease and toxin management strategies. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Kang and postdoc Ningxiao Li attended the Fungal Genetics Conference in Asilomar in March 2019, in which Ningxiao participated in a grant writing workshop. Ningxiao Li mentored an undergraduate student, Amy Kovaleski, via a project that aims to screen and identify secreted fungal metabolites that inhibit the production of aflatoxins, a group of fungal toxins that pose grave health threats around the world. Ningxiao also helped Amy to prepare a research proposal to the College of Agricultural Sciences at Penn State, which resulted in $2,000 to support her research during 2019/2020. Geiser and PhD student Terry Torres-Cruz attended the Mycological Society of America Conference at the University of Minnesota in August, 2019. Geiser presented a symposium presentation on the history and current status of genealogical methods to infer species boundaries in Fungi, and Torrez-Cruz presented a poster on a unique Guyanan Fusarium species that induces pseudoflower formation on its yellow-eyed grass host. Geiser and PhD students Emma Wallace and Terry Torres-Cruz instructed and participated in the Fusarium Laboratory Workshop at Kansas State University in June, 2019. Geiser, Wallace and Torres-Cruz, presented a Fusarium mini-workshop at the American Phytopathological Society Northeast Division meeting in April, 2019. Participants were able to observe living cultures of over 20 common Fusarium species, along with lectures on Fusarium identification and systematics. Two students from the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa, visited Geiser's lab from July-September, 2019, working on Fusarium interactions with plant hosts. In addition, an undergraduate in the Biotechnology Engineering Program at the Technical University of Costa Rica started in Geiser's lab in September 2019, working with Torres-Cruz and Geiser on diagnostic methods for emerging Fusarium tomato pathogens. PhD students Torres-Cruz and Wallacetraveled to South Africa, presenting their research plans at the Southern African Society for Plant Pathology meeting, and touring Plant Pathology facilities at the University of Stellenbosch and the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria. This opportunity provided them with new perspectives on agriculture and plant pathology, involving a variety of cropping systems on the African continent that are fundamentally different from those familiar to us in the USA. How have the results been disseminated to communities of interest?Besides the papers noted above, Kang presented the work on volatile-mediated fungal interactions with other organisms in a concurrent session during the 2019 Fungal Genetics Conference and gave a seminar at Seoul National University in Korea. Jiménez-Gasco also presented research on the ecological and genetic diversity of plant-associated F. oxysporum at the USDA Symposium on Phytobiomes and Population Biology held at the USDA-ARS Beltsville Agricultural Research Campus, Beltsville, MD in June 6, 2019. Over 50 USDA researchers participated in this event. What do you plan to do during the next reporting period to accomplish the goals?Kang will employ metabolomics and transcriptomics tools to investigate how VCs produced by F. oxysporum and other fungi affect other microbes at the molecular level and to identify novel biologically active compounds that play crucial roles in biocontrol and microbial ecology. Geiser will complete work on a phylogenomic study revealing core genome lineages within F. oxysporum. There will be at least one more Fusarium laboratory mini-workshop in 2019, at the University of Florida, training individuals in basic identification of Fusarium species in culture. We will make progress in recognizing and describing new species within the Fusarium sambucinum Species Complex, the major group of trichothecene mycotoxin producing Fusarium, and clarify the taxonomy of Fusarium species associated with emerging tomato diseases in the US and Mexico. Jiménez-Gasco will complete work on the diversity of endophytic populations of Fusarium oxysporum. Specifically, she will focus on exploring phylogenetic signals of adaptation to specific hosts in populations of endophytes associated with chickpea, banana and tomato using newly developed markers that are based on core genome sequences.

Impacts
What was accomplished under these goals? Goals 1b, 2a and 2b: Geiser and undergraduate Shawn Chang integrated 41-locus data derived from complete genome sequences of an additional 72 isolates of the F. oxysporum Species Complex, adding to the ~100 previously assembled, producing a detailed picture of diversity of this important species complex. Goals1b, 2a and 2b: Geiser and previous PhD student Christopher Smyth discovered that the fungus F. keratoplasticum a human pathogen that also causes sea turtle egg fusariosis, is a common component of beach sands in association with sea turtle nests. This provides new knowledge about the ecological niche for this important fungus. Goal 1b: Jiménez-Gasco, Geiser and previous PhD student Freddy Magdama evaluated current molecular methods available in the literature for the diagnosis of Fusarium oxysporum f. sp. cubense Tropical Race 4 threatening banana production worldwide. Phylogenetic analyses, VCG testing, sequence comparison, and pathogenicity tests suggest the presence of non-target F. oxysporum isolates that share genomic regions with pathogenic strains but lack true pathogenicity to banana. The findings of this work are of foremost importance for international regulatory agencies performing surveillance tests in pathogen-free areas using the current diagnostic methods. Goals 3a and 3b: Kang uncovered a novel mechanism that may potentially play an important role in Trichoderma-based biocontrol and fungal-fungal interactions. Trichoderma virens and T. viride significantly increased the amount/activity of secreted antifungal metabolites in response to volatile compounds (VCs) produced by 13 strains of Fusarium oxysporum. However, T. asperellum did not respond to any, while T. harzianum responded to VCs from only a few strains. Gene expression analysis showed up-regulation of several biocontrol-associated genes in T. virens in response to F. oxysporum VCs. Analysis of VCs from seven F. oxysporum strains identified six VCs that are produced by all of them. All four Trichoderma species produced VCs inhibitory to F. oxysporum. F. oxysporum also recognizes Trichoderma spp. by sensing their VCs and releases VCs that inhibit Trichoderma, suggesting that both types of VC-mediated interaction are common among fungi. Goals 3a and 3b: Kang also investigated how VCs produced by F. oxysporum and several Verticillium species affect plants' ability to manage biotic and abiotic stresses. Both Fusarium oxysporum and several Verticillium species infect diverse plants and caused vascular wilt diseases. Kang has been studying the mechanism of pathogenicity employed by both pathogens and their ecology. Insights from research on Verticillium species will help understand and manage diseases caused by F. oxysporum and vice versa. Two papers based on Verticillium species are noted under Other Products.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Wang, W., Li, N., Liu, X., and Kang, S. (2019) I Plate-based Assay for Studying How Fungal Volatile Compounds (VCs) Affect Plant Growth and Development and the Identification of VCs via SPME-GC-MS. Bio-Protocol 9: e3166.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Li, N., Alfiky, A. Wang, W., Islam, M., Nourollahi, K., Liu, X., and Kang, S. (2018) Volatile compound-mediated recognition and inhibition between Trichoderma biocontrol agents and Fusarium oxysporum. Frontiers in Microbiology 9: 2614.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Li, N. and Kang, S. (2018) Do volatile compounds produced by Fusarium oxysporum and Verticillium dahliae affect stress tolerance in plants? Mycology 6: 166-175.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Smith, C.W., Sarmiento-Ram�rez, J.M., Short, D.P.G., Di�guez-Uribeondo, J., ODonnell, K. and Geiser, D.M. (2019) Unraveling the ecology and epidemiology of an emerging fungal disease, sea turtle egg fusariosis. PLoS Pathogens 15: e1007682.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Magdama, F., Monserrate-Maggi, L., Serrano, L., Sosa, D., Geiser, D.M., and Jim�nez-Gasco, M. (2019) Comparative analysis uncovers the limitations of current molecular detection methods for Fusarium oxysporum f. sp. cubense race 4 strainsPLoS ONE 14(9): e0222727.

Progress 07/01/18 to 09/30/18

Outputs
Target Audience:Fundamental and applied researchers, clinicians and stakeholders in industry, government and academic institutions studying plant diseases, mycotoxins and fungal genomics and evolution. We seek taxonomic clarity in Fusarium that will assist efforts to detect, monitor and manage Fusarium disease and toxin issues. We seek improved understanding of the ecological, molecular and genomic underpinnings of the evolution and emergence of new Fusarium pathogens and diseases, with the goal of facilitating the discovery of novel disease and toxin management strategies. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Geiser, PhD students Terry Torres-Cruz and Emma Wallace attended a diversity symposium at the International Mycological Congress, August 2018. How have the results been disseminated to communities of interest?Geiser co-hosted and presented in a symposium on Fusarium Phylogenomics with Prof. Brenda Wingfield, University of Pretoria, at the International Mycological Congress, August 2018. What do you plan to do during the next reporting period to accomplish the goals?1. Make significant progress in the development of the new version of the FusariumID database (Goal 2). 2. Complete a phylgenomic analysis of the Fusarium oxysporum Complex (Goal 1b).

Impacts
What was accomplished under these goals? 1. 41 informative core genome marker loci were extracted from additional complete genome sequences of pathogenic and non-pathogenicF. oxysporum isolates from diverse plant hosts, to be added to an existing database of over 100 isolates. This work will provide the largest and most robust phylogenetic picture of F. oxysporum to date, and facilitate diagnostics and better understanding of the relationships between pathogens and non-pathogens (Goal 1) 2. Primers were designed for PCR and Sanger sequencing that target a subset of five highly informative core genome markers within F. oxysporum, permitting diagnostic and phylogenetic analysis of these pathogens at a fine scale without the need for complete genome sequences. (Goal 2) 3. Barcode sequence data (TEF locus) were completed for a set of over 300 indoor Fusarium isolates collected around the US, that will provide the first DNA-based study of indoor Fusarium diversity on this scale. (Goal 2) 4. Tables of Fusarium names organized by Species Complex were compiled, giving Fusarium taxonomy users a resource for cross-referencing names and phylogenetic positions of taxa. (Goal 2)

Publications