CHARACTERIZING THE BIODIVERSITY (GENETIC, GENOMIC, AND SYSTEMATIC) OF RUST FUNGI

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1010662
• Project Start Date: Oct 14, 2016
• Project End Date: Sep 30, 2021
• Program Code: [(N/A)]- (N/A)

Recipient Organization
PURDUE UNIVERSITY
(N/A)
WEST LAFAYETTE,IN 47907

Performing Department
Botany & Plant Pathology

Non Technical Summary
Rust fungi (Basidiomycota, Pucciniomycotina, Pucciniales) are the largest natural group of fungal plant pathogens containing ca. 8000 described species in more than 150 genera that comprise nearly one-third of all known basidiomycetes (Savile 1976, Kirk et al. 2001, Aime et al. 2006). All are obligate parasites that cannot grow outside of host tissues. Rust fungi are phenotypically and genetically plastic organisms that have the most complex life cycles in the kingdom Fungi, and possibly of any eukaryotes (Laundon 1973, Hennen and Buriticá 1980, Cummins and Hiratsuka 2003). The rust life cycle can involve up to five or six different spore types that vary in function, morphology, and nuclear composition, and may require alternation between two unrelated host plants for completion (Hiratsuka and Hiratsuka 1980, Bruckart et al. 2010). Life cycles, the process of sexual recombination if it occurs, host specificity and virulence vary from genus to genus and species to species and even isolate to isolate (Savile 1976, Cummins and Hiratsuka 2003). Even genome size is quite variable, with haploid size-estimates ranging from 64Mbp to 418Mbp just for some species in the family Pucciniaceae (Aime et al. 2014). Rust diseases cause serious economic damage worldwide on agricultural, forest and ornamental plants, resulting in billions of dollars' worth of damage each year. A few examples include serious disease agents of sugarcane (caused by the rust Puccinia melanocephala), soybean (Phakopsora pachyrhizi), and wheat (Puccinia graminis) and the limiting factors to coffee (Hemileia vastatrix) and pearl millet production (Puccinia substriata) worldwide. Because of the presumed host-specificity of some species, they also offer a potential source of biological control organisms for noxious and invasive weeds (McCain et al. 1990, Evans 1993). Yet, despite their global importance, for the majority of rust species, complete life cycle data, including host-range (i.e., alternative hosts, or plants related to the primary host that can also be host to the same spore stages as the primary host), geographic distribution, cytology, identity of alternate hosts (i.e., the host, unrelated to primary host, that is necessary for completion of life cycle for many rusts), and/or mode of sexual reproduction, are incomplete (Savile 1976, Ono and Hennen 1983, McCain et al. 1990, Hennen and McCain 1993). A further complication to the study of rusts is that no universal classification for these fungi has yet been accepted. Taxonomy and even family-level classification for rusts is contentious (Hennen and Buriticá 1980, Ono and Hennen 1983) and requires further investigation (Kirk et al. 2001) and species concepts and identifications are based on problematic morphological characters that are known to be plastic and may not have phylogenetic or even diagnostic value.Finally, while diagnosing most other groups of important plant pathogens has been largely redefined and informed by molecular data and methods over the past ten years, identification of rust fungi is still reliant on morphology and host, despite documented problems with this system--to make just one example, urediniospore morphology for some rust species was shown to be influenced by which alternative host was utilized by the rust, rather than being species-determined (Long 1914). These difficulties continue to lead to misidentification of species which has plagued the rust literature for almost 100 years. None the less there is at present a lack of rust-specific molecular biology protocols for even the most basic molecular genetics (such as, for example, protoplasting techniques, transformation system, or selectable markers).A combination of molecular approaches is needed to address these problems. Systematics is the study of biological diversity and the relationships of organisms. Molecular phylogenetics (the science of applying molecular characters toward uncovering systematic relationships) has been used to identify invasive phytopathogens for which even placement in a phylum via morphology is uncertain (e.g., Aime and Phillips-Mora 2005), to distinguish new invasive phytopathogens from morphologically similar resident relatives (e.g., Aime and Rossman 2007), and to match different spore stages of the same species on different hosts, thus completing life-cycle and host range data for cryptic macrocyclic rust species (e.g., R. Peterson, P. Crane, and M.C. Aime, unpublished).

Animal Health Component

(N/A)

Research Effort Categories

Basic

90%

Applied

(N/A)

Developmental

10%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
212	4020	1102	75%
212	4020	1040	25%

Knowledge Area
212 - Pathogens and Nematodes Affecting Plants;

Subject Of Investigation
4020 - Fungi;

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

Keywords

fungi

pucciniales

herbaria

collections

systematics

rust fungi

Goals / Objectives
To increase the rust fungus collections of the Arthur Fungarium through field collections and collaborators.To identify, catalog, and create an online publically accessible database of rust fungi in the Arthur Fungarium.To use molecular systematics to develop a phylogenetic framework for Pucciniales that will allow prediction of biology and host associations.To develop molecular tools (e.g., DNA barcodes, SSR markers) that will allow rapid identification and/or monitoring of rust fungi of interest at the level of species and/or population/race.

Project Methods
Increase rust fungus collections. The PI and the Arthur Fungarium are known worldwide as a global resource for the identification and study of rust fungi and receive hundreds to thousands of specimens and accessions from around the globe annually. Field sampling will be concentrated in tropical, especially neotropical, regions of the world. Firstly, these regions are precisely those that have been historically undersampled and are predicted to contain numerous species new to science; secondly, rusts originating from these regions are most likely to be the source of invasive exotic disease in the US. USDA-APHIS-PPQ permits that specifically allow for the importation of dried rust fungi from around the world have been obtained and the PI has extensive experience working with local permitting agencies to obtain collecting and export permits. Collection techniques employed in the field will follow those developed and utilized by the PI over the last 20 years for both accessible and remote regions (e.g. Toome & Aime 2015, Aime et al. 2014).Catalog and create online database. Current specimens and new accessions will be cataloged in Specify 6.5, which is housed on a dedicated server. Specify uses MySQL and has been designed specifically for museum and herbarium specimens, and includes important features such as tracking of nomenclatural changes and specimen transactions. Using Specify, data can easily be imported and exported from/to Excel allowing easy sharing of data and conversion into other formats, such as XML. After cataloging data will be incorporated into the Mycology Collections Portal (MycoPortal) enabling streamlined access to all data by any outside researcher. The MyCoPortal utilizes the open source software package, Symbiota through the Integrated Digitized Biocollections (iDigBio) network, funded by the National Science Foundation (https://www.idigbio.org/about-idigbio).Develop a phylogenetic framework for studying Pucciniales. DNA from rust fungi have been found to degrade rapidly in comparison to other Asco- and which makes the acquisition of fresh material for DNA-based molecular studies particularly important. A broad-based sampling is required for initial work to develop a robust backbone phylogeny for the rusts. Newly acquired rust samples (from field collecting and selected herbarium specimens) will be extracted, amplified, and sequenced following protocols developed in Aime (2006 and unpublished). Sequencing reactions will be edited and contiguous sequences assembled in Sequencher (Gene Codes Corp., Ann Arbor, MI). Sequence alignments for each gene will be constructed in MAFFT or MUSCLE and adjusted by eye (e.g., Toome & Aime 2015). 28S genes will be examined within an assembled dataset of more than 1000 rust sequences (Aime 2006 and unpublished) that include representative taxa from all 13 Pucciniales families fide Cummins and Hiratsuka (2003); representative taxa from 58 of 128 rust genera fide Cummins and Hiratsuka (2003); and ~700 rust species. 18S genes will be examined within a dataset of 180 rust sequences (Aime 2006 and unpublished) that include representatives for all 13 Pucciniales families fide Cummins and Hiratsuka. Sequences will be analyzed in combined and single gene analyses using maximum parsimony and neighbor-joining analyses in Paup* v.4.0b10 (Swofford 2002) in the manner of Aime (2006), by Maximum Likelihood methods such as RAxML and by Bayesian analyses using MrBayes 3.0 (Ronquist and Huelsenbeck 2003) following Aime et al. (2006, 2014). Resolved phylogenetic trees will be used to evaluate the genetic relatedness and evolutionary relationships among the rusts, and to make predictions about plant-pathogen interactions and host range and life cycle for the thousands of rusts for which these data are missing or incomplete. Resolved phylogenetic trees will be used to test various hypotheses regarding rust fungal evolution using a variety of methodologies. For example estimations of divergence times for nodes of major Pucciniales lineages will be calculated using a secondary calibration procedure in BEAST v.1.7.5 (Renner 2005, Drummond et al. 2006; Drummond & Rambaut 2007) for the molecular dating of these fungi as they lack a robust fossil record (Matheny et al. 2009; Wilson et al. 2012). Evaluation of the co-evolutionary complexity between the Pucciniales and their hosts will be using Jane 4 (Conow et al., 2010). Ancestral character traits for different nodes of interest will be reconstructed by Bayesian statistics using BayesTraits v2.0 (http://www.evolution.reading.ac.uk/BayesTraits.html).Develop molecular tools. In addition to phylogenetic analyses, sequence data generated for this project will be used to develop rapid methods for identification of rusts. Locally based BLAST databases will be developed for web-based interactive identification methods. Barcodes can be used for connecting alternate states of rust fungi (which can produce up to six morphologically dissimilar spore stages on two or more host plants, making elucidation of individual species very difficult and incomplete for most). Barcodes may also be used to track movement of species of interest. Recently the mycological community has selected the ITS as the region of preference for use in fungal barcoding (Schoch et al. 2012), while recognizing that ITS alone may not work for all groups of fungi. Initial efforts will be aimed at evaluating the ITS region for suitability as a rust DNA barcode.If rDNA gene regions do not provide meaningful DNA barcoding data, then alternate methods, such as ITS2 secondary structure (Landis & Gargas 2007), or genes, such as single copy protein genes, will be analyzed for their potential as barcoding tools. A list of 76 candidate genes for fungal phylogenetic analyses has been compiled by the Assembling the Fungal Tree of Life initiative (NSF DEB 0732968); which may be evaluated across the fungi for their use at differing phylogenetic levels of inquiry and universal fungal primers are being designed and will be used as a source of additional barcode regions for testing. Additional loci may be mined and tested from the phylogenomic study of Dentinger et al. (2016). Methods for barcoding rust fungi will follow recommended protocols established by UNITE, i.e., (1) fungal specimens from which DNA are extracted will be deposited in established herbaria (LSU); (2) only specimens that are well-developed and show all the stages necessary for accurate identification will be used as sources of DNA; (3) sequenced specimens will include the name of the expert who made the identification; (4) DNA samples will be saved along with the voucher specimen; (5) sequences will be associated with specimen data; (6) specimens from which DNA is derived will be illustrated whenever possible.Whole genome data may be generated for species of interest using protocols already established in the PIs lab (e.g., Padamsee et al. 2012, Toome et al. 2014). Genomes will be mined for microsatellite loci utilizing a set of Perl scripts designed for this purpose (Diaz-Valderrama and Aime 2016) and data generated using a modified M13 method (Schuelke 2000, Diaz-Valderrama and Aime 2016).

Progress 10/14/16 to 09/30/21

Outputs
Target Audience:The target audience for this research is the international community of professional mycologists, biologists and systematistsas well as plant pathologists, extension agents, plant breeders, and other agricultural scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has helped to train one technician, 8 undergraduate students, 2 interns, 2 graduate students, and one post doc on identifying rust fungi in the PIs lab. How have the results been disseminated to communities of interest?Results have been dessiminated through peer reviewed publication and several rust talks to the general public and citizen scientist community in the US and abroad. Data have been disseminated through the MycoPortal and GenBank and the rust barcode site. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1: To increase the rust fungus collections of the Arthur Fungarium through field collections and collaborators. The first goal of this project was to increase rust fungus collections of the Arthur Fungarium at Purdue. These collections are known worldwide as a global resource for the identification and study of rust fungi. >50,000 specimens were added to PUR through: Targeted field sampling by the PI primarily from remote tropical locales that had not been previously sampled, or poorly sampled, for rust fungi. This work was supported by numerous federally funded (National Science Foundation, National Geographic) grants. Newly accessioned material sent from around the world (from students, researchers, and diagnosticians) for identification and/or vouchering for publication. Repatriation of ca 30,000 specimens from BRIT in Ft. Worth Texas. This objective has resulted in ~ 20 papers on new species or new distributions of rust fungi. Objective 2: identify, catalog, and create an online publicly accessible database of rust fungi in the Arthur Fungarium. The second goal was the creation of a molecular resource for the identification of rust fungi. This was accomplished through funding from the USDA. Achievements include: DNA barcoding of 5000+ authentic specimens of rust fungi at the 28S locus, all with associated metadata and vouchered specimens. Verification of all names and sequences associated with this material. Creation of a blastable online resource for the identification of rust fungi from authentic, verified, and vouchered material (http://rustblast.aimelab.geddes.rcac.purdue.edu/). The publication announcing the website has been drafted but not yet submitted for publication. Objective 3: To use molecular systematics to develop a phylogenetic framework for Pucciniales that will allow prediction of biology and host associations. The third goal is the creation of a phylogenetic framework for the rust fungi. This was accomplished with the publication, in 2020 (Aime & McTaggart 2020), of the first higher rank revision of the rust fungi to be published in 40 years. This paper was the cumulation of 16 years of work, resolved the deeper phylogenetic nodes, and stabilized the taxonomy of the order. This paper was supported by 25+ additional nomenclatorial, taxonomic, phylogenetic, and biological papers on rust fungi during the entire Hatch project (see list of publications). Objective 4: To develop molecular tools (e.g., DNA barcodes, SSR markers) that will allow rapid identification and/or monitoring of rust fungi of interest at the level of species and/or population/race. The PI has established a collaboration with Two Blades (Norwich, UK) to develop molecular markers for genotyping and population genetics of Phakopsora pachyrizi, the causal agent of Asian soybean rust. With funding from World Coffee Research and the International Institute for Cooperation in Agriculture, our lab developed the first genotyping markers for Hemileia vastatrix, the causal agent of coffee leaf rust (CLR) disease. Some achievements include: This project has attracted and trained several post docs, interns, and students from developing countries (Kifle, Luis Ramirez, Cristhian Ruiz, Carmen The reproductive biology of H. vastatrix was finally determined (Ramirez et al. 2021) When CLR was discovered in Hawaii in Oct. 2020, our lab was consulted for identification and to trace origins of the outbreak (Ramirez et al., submitted). Our ability to respond rapidly to CLR in Hawaii made it possible to secure ~8M in federal funds with colleagues in Hawaii and Puerto Rico.

Publications

• Type: Journal Articles Status: Awaiting Publication Year Published: 2021 Citation: Crous, P, Rossman A, Aime MC, Allen WC, Burgess T, Groenewald JZ, Castlebury LA. 2021. Names of phytopathogenic fungi: a practical guide. Phytopathology [invited review]: submitted 11-20. in press
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Duplessis S, Lorrain C, Petre B, Figueroa M, Dodds PN, Aime MC. 2021. Host adaptation and virulence in heteroecious rust fungi. Annual Review of Phytopathology 59: 403-422.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2021 Citation: Rami?rez-Camejo LA, Eamvijarn A, Di?az-Valderrama JR, Karlsen-Ayala E, Johnson E, Pruvot-Woehl S, Meija LC, Montagnon C, Aime MC. Global analysis of Hemileia vastatrix populations shows clonal reproduction for the coffee leaf rust pathogen throughout most of its range. Phytopathology: In press.
• Type: Journal Articles Status: Published Year Published: 2021 Citation: Rhiney K, Guido Z, Knudson C, Avelino J, Bacon CM, Leclerc G, Aime MC, Bebber DP. 2021. Epidemics and the future of coffee production. PNAS 118 (27): e2023212118 10.1073/pnas.2023212118.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Aime MC, McTaggart AR. 2020 [2021]. A higher rank classification for rust fungi, with notes on genera. Fungal Systematics and Evolution 7: 2147.
• Type: Journal Articles Status: Published Year Published: 2021 Citation: G�mez-Zapata P, Haelewaters D, Quijada L, Pfister DH, Aime MC. 2021. Notes on Trochila (Ascomycota, Leotiomycetes), with new species and combinations. MycoKeys 78:21-47.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2021 Citation: Okane I, Ono Y, Ohmachi K, Aime MC, Yamaoka Y. Desmella lygodii comb. nov., a rust fungus of Lygodium species. Mycoscience: accepted 6-21.

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

Outputs
Target Audience:The target audience for this research is the international community of professional mycologists, biologists and systematistsas well as plant pathologists, extension agents, plant breeders, and other agricultural scientists. Changes/Problems:All major problems are related to either COVID, or lack of actual funding to do the proposed work. Regarding COVID, the subsequent shut down of our facilities for several months, limited reopening with lack of floor space have reduced our work capacity by at least 75% (as we do not have enough physical space to allow more than 2 people to work at a time with social distancing). Lack of any funding has severly crippled our abilities to deal with coffee rust. However, funding through the farm bill has allowed us to add a DNA barcoding aspect to the project. What opportunities for training and professional development has the project provided?This project has helped to train one technician, seven undergraduate students, 2 graduate students, and one post doc on identifying rust fungi in the PIs lab. How have the results been disseminated to communities of interest?Results have been dessiminated through peer reviewed publication and several rust talks to the general public and citizen scientist community in Colorado, California, Indiana and the east coast. Data have been disseminated throughthe MycoPortal and GenBank. What do you plan to do during the next reporting period to accomplish the goals?Two major publications will be completed/published: A systematic revision of rust fungi classification, and a completely updated Illustrated Genera of the Rust Fungi. Additionally, through funding, a DNA barcode library for identification will be developed for several thousand rust fungi.

Impacts
What was accomplished under these goals? 1. Rust collections were increased, including new representation from tropical locales including India, Guyana, and Peru. 2. All currently accessioned Arthur herbarium holdings are published and searchable online, including digitized images of all (ca. 5000) type specimens. 3. Goal 3 has been completed and the paper is currently under revision. In addition, the book, The Illustrated Genera of Rust Fungi, is currently being revised by the PI and will be published by APS press in 2021. 4. Protocols and primers have been developed for three rust fungus loci; SSR markers have been developed for coffee leaf rust; funding has been obtained from USDA-PPQ to develop DNA barcodes for 3000 species or rust fungi to be completed in 2021.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Amoako-Attah I, Shahin AS, Aime MC, Odamtten GT, Cornelius E, Nyaku ST, Kumi-Asare E, Yahaya HB, Bailey BA. 2020. Identification and characterization of fungi causing thread blight diseases on cacao in Ghana. Plant Disease. doi: 10.1094/PDIS-03-20-0565-RE
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Bruckart WL, Thomas JL, Abbasi M, Aime MC, Frederick RD, Tancos MA. 2020. Uromyces rebeccae sp. nov., a newly described rust on the federally endangered plant, California sea-blite (Suaeda califonrinica). Mycologia 112:543-551. : doi: 10.1080/00275514.2020.17.1739602
• Type: Journal Articles Status: Published Year Published: 2020 Citation: D�az-Valderrama JR, Leiva-Espinoza ST, Aime MC. 2020. The history of cacao and its diseases in the Americas. Phytopathology: doi: 10.1094/PHYTO-05-20-0178-RVW
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Lendemer J, Thiers B, Monfils AK, Zaspel J, Ellwood ER, Bentlley A, Levan K, Bates J, Jennings D, Contreras D, Lagomarsino L, Mabee P, Ford LS, Guralnick R, Gropp RE, Revelez M, Cobb N, Seltmann K, Aime MC. 2020. The extended specimen network: A strategy to enhance US biodiversity collections, promote research and education. Bioscience 70:2330. doi: 10.1093/biosci/biz140
• Type: Journal Articles Status: Published Year Published: 2020 Citation: L�cking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, �pik M, Robert V, Seifert KA, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. 2020. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal barcoding? IMA Fungus 11:14. doi: https://imafungus.biomedcentral.com/track/pdf/10.1186/s43008-020-00033-z
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Molina L, Rajchenbrg M, de Errasti A, Aime MC, Pildain MB. 2020. Sapwood-inhabiting mycobiota and Nothofagus tree mortality in Patagonia: Diversity patterns according to tree species, plant compartment and health condition. Forest Ecology and Management 462: 117997. doi: 10.1016/j.foreco.2020.117997
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Prasanna AN, Gerber D, Kijpornyongpan T, Aime MC, Doyle V, Nagy LG. 2020. Model choice, missing data, and taxon sampling impact phylogenomic inference of deep Basidiomycota relationships. Systematic Biology 69: 1737. https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz029/5486399
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Song J, Aime MC, Xu B. 2020. Puccinia xinyuanensis sp. nov., the causal agent of rust on wild tulip (Tulipa iliensis) in China. Phytotaxon 459: 8792. doi: 10.11646/phytotaxa.459.1.10
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Aime MC, Rossman AY, Ono Y, Castlebury LA. 2019. (2688) Proposal to conserve the name Phakopsora (Basidiomycota, Pucciniales) with a conserved type. Taxon 68:592. doi: 10.1002/tax.12076
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Aime MC, Rossman AY, Ono Y, Castlebury LA. 2019. (2689-2690) Proposals to conserve the names Phakopsora pachyrhizi against Uredo erythrinae and U. sojae (Malupa sojae) and Physopella meibomiae (Phakopsora meibomiae) against Aecidium crotalariicola, U. teramni, and U. vignae (M. vignae) (Basidiomycota, Pucciniales). Taxon 68:593-594. doi: 10.1002/tax.12077
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Pisani C, Patel PC, Rosskopf EN, Abbasi M, Aime MC. 2019. First report of downy mildew caused by Plasmopara halstedii on Ageratum houstonianaum in Florida. Plant Disease: In press. doi: https://apsjournals.apsnet.org/doi/pdf/10.1094/PDIS-06-19-1331-PDN
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Rosskopf EN, Abbasi M, Aime MC. 2018. First report of guineagrass smut caused by Conidiosporomyces ayresii in North America. Plant Disease: doi: 10.1094/PDIS-08-18-1410-PDN
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Rush TA, Golan J, McTaggart A, Kane C, Schneider RW, Aime MC. 2019. Variation in the internal transcribed spacer region of Phakopsora pachyrhizi and implications for molecular diagnostic assays. Plant Disease 103: 2237-2245. doi: 10.1094/PDIS-08-18-1326-RE

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

Outputs
Target Audience:The target audience for this research is the international community of professional mycologists, biologists and systematistsas well as plant pathologists, extension agents, plant breeders, and other agricultural scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?Results have been dessiminated through peer reviewed publication and through the MycoPortal. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. Rust collections were increased, including new representation from tropical locales including Ethiopia and Panama.2. Marker development proceeded for population-genetics of H. vastarix..

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Bruckart WL, Thomas JL, Frederick RD, Aime MC, Abbasi M. 2019. First report of a rust disease caused by Uromyces sp. on Suaeda californica in California. Plant Disease: In press.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Ishaq A, Aime MC, Sadiqullah, Afshan NuS, Fiaz M, Niazi AR, Khalid AN. 2019. First report of Asian pistachio rust (Pileolaria pistachiae) in Pakistan. Canadian Journal of Plant Pathology: in press.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Ullah S, Abbasi M, Khalid AN, Ishaq A, Fiza M, Aime MC. 2019. Allodus prostii comb. nov., causal agent of tulip rust. Nova Hedwigia 109: 225-232.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:The target audience for this research is the international community of professional mycologists, biologists and systematists as well as plant pathologists, extension agents, plant breeders, and other agricultural scientists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided the training for fourundergraduate students and one technician in molecular mycology and herbarium/museum sciences. How have the results been disseminated to communities of interest?Yes. What do you plan to do during the next reporting period to accomplish the goals?further develop our (the community's) ability to sequence and annotate entire rust genomes for further development of identification tools, tools for analyzing population biology and epidemiology, and tools for understanding the evolutionary history of the rust fungi.

Impacts
What was accomplished under these goals? 1. Rust collections were increased, including new representation from many tropical locales including Vanuatu, Cameroon, Bolivia, etc. 2. All the specimens in the Arthur Fungarium have now been catalogued and are available through MycoPortal:http://mycoportal.org/portal/index.php 3. Several key papers on evolutionary origins of rust life cycle (Aime et al. 2018a) and heteroecism (Scholler et al. 2018) were published, as was a review on the overall phylogenetics and phylogenomics of rust fungi (Aime et al. 2018b). 4. Successful SSRs have been developed for exploring population biology of one economically important rust, Hemileia vastatrix; a collaborative proposal that will allow for the genome sequencing of 50 select species of rusts have been supported by the Joint Genome Institute.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Aime MC, Abbasi MA. 2018. Puccinia modiolae in North America: distribution and natural host range. MycoKeys 39:6373. doi: 10.3897/mycokeys.39.27378
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Aime MC, Bell C, Wilson AW. 2018. Deconstructing the evolutionary complexity of rust fungi (Pucciniales) and their hosts. Studies in Mycology 89:143152. doi: 10.1016/j.simyco.2018.02.002
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Aime MC, Castlebury L, Abbasi M, Begerow D, Berndt R, Kirschner R, Maravanov� L, Ono Y, Padamsee M, Scholler M, Thines M, Rossman AY. 2018. Recommendations of generic names competing for use: Pucciniomycotina and Ustilaginomycotina, Basidiomycota. IMA Fungus 9: 7590. doi: 10.5598/imafungus.2018.09.01.06
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Davis DD, Harvey RJ, Aime MC. 2018. New records of rust disease caused by Uromyces halstedii in North America. Plant Disease 102: 2382. doi: 10.1094/PDIS-02-18-0261-PDN
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Kenaley SC, Quan M, Aime MC, Bergstrom GC. 2018. New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States. Mycological Progress 17:1251-1267. doi: 10.1007/s11557-018-1434-1
• Type: Journal Articles Status: Published Year Published: 2018 Citation: McTaggart AR, Aime MC. 2018. The species of Coleosporium (Pucciniales) on Solidago in North America. Fungal Biology 122: 800809. doi: 10.1016/j.funbio.2018.04.007
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Mohali SR, Aime MC. 2018. First report of gladiolus rust caused by Uromyces transversalis in Merida, Venezuela. Plant Disease 102: 444445. doi: 10.1094/PDIS-07-17-0093-PDN
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Scholler M, Lutz M, Aime MC. 2018. Repeated formation of correlated species in Tranzschelia (Pucciniales). Mycological Progress: in press. doi: 10.1007/s11557-018-1417-2

Progress 10/14/16 to 09/30/17

Outputs
Target Audience:19 Purdue undergraduate students through formal classroom and laboratory instruction; 515 international scientistsand 30 national diagnostitiansduring invited presentations at workshops (extension and outreach) in Madison WI, West LafayetteIN, and Asilomar CA; 700 international scientists and students during invited presentations in Utrecht (Netherlands) andQueretaro (Mexico). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project has provided the training for two undergraduate students and one technician in molecular mycology and herbarium/museum sciences. How have the results been disseminated to communities of interest?Dr. Aime has published 11 peer-reviewed research papers and one book chapterin 2017, of which five resulted directly from this project. She and her students have given 11 invited presentations in 2017 (in Ohio, Mexico, Indiana, the Netherlands, Peru, Wisconsin, and California), and 22 contributed presentations. Of these, two were for rust fungal workshops, including one workshop for diagnosticians. What do you plan to do during the next reporting period to accomplish the goals?Activities conducted during the second year of this project will focus on continuing to build the Arthur Fungarium as a center of expertise on rust fungi through data collection: (1) broadening collection of rust fungi to other unexplored regions in the tropics; (2) and conducting molecular sequencing of pathogens and analyzing those data; (3) developing expertise in rust fungal genomics; and (4) the dissemination of knowledge via mentoring of undergraduate and graduate students.

Impacts
What was accomplished under these goals? The first goal of this project is to increase rust fungus collections of the Arthur Fungarium at Purdue. These collections are known worldwide as a global resource for the identification and study of rust fungi. Field sampling over the last period was concentrated in tropical, especially remote, regions of the world, increasing the PUR holdings by nearly 1000 specimens including new species. A second goal is the creation of a molecular resource for the identification of rust fungi. The first global multi-gene analysis of rusts that examines their coevolution with land plants has been completed and submitted for publication. The third goal is the creation of a phylogenetic framework for the rust fungi; to this end a global analysis of family-level divisions is being prepared for publication, and a second paper concerned with stabilizing generic-level taxonomy has been submitted.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Abbasi M, Aime MC, Eamvijarn A, TC Creswell, GE Ruhl, Wright S. 2017. First report of rust disease caused by Cronartium quercuum on Chinquapin oak in North America. Plant Disease 101:1329.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Ishaq A, Afshan NS, Niazi AR, Aime MC, Khalid AN. 2017. First report of rust caused by Pucciniastrum guttatum on Gallium sp. from Pakistan. Plant Disease 101:245.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Mohali SR, Aime MC. 2017. First report of gladiolus rust caused by Uromyces transversalis in Merida, Venezuela. Plant Disease: doi: 10.1094/PDIS-07-17-0093-PDN
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Abbasi M, Aime MC. 2016. Two new Puccinia species on Melica (Poaceae) from USA. Mycotaxon 131:247-253.
• Type: Book Chapters Status: Awaiting Publication Year Published: 2017 Citation: Aime MC, McTaggart A, Mondo SJ, Duplessis S. 2017. Phylogenetics and phylogenomics of rust Fungi. In: Advances in Genetics and Genomics. In press 10-2017.