Diversity of Plant-Pathogenic Fungi PLHL 7051 Course Syllabus Fall 2013

Instructors: Vinson Doyle Sebastian Albu Life Sciences Building, LSB 261 [email protected] [email protected]

Tuesday (Seminar Discussion/Other): 1:30-2:30 PM (LSB A465) Tuesday (Lab): 2:30-5:30 PM (LSB 308) Wednesday (Lecture): 1:00-3:00 PM (LSB A465)

Grading: Lecture/Lab/Seminar Participation: 25% Lab Notebook: 25% Fungal Wiki: 25% Collections: 25%

Lecture material will be drawn from multiple sources. However, the following are good references: 1. C.J. Alexopoulos, C.W. Mims and M. Blackwell. 1996. Introductory . Fourth Edition. J. Wiley & Sons. New York. 2. J. Webster and R. Weber. 2007. Introduction to Fungi. Third Edition. Cambridge University Press

Lecture (Fundamental): Mycology is the study of fungi. The primary goal of the lecture will be to highlight the fundamentals of fungal biology through an exploration of fungal diversity. Whether your interest is in fungi in general or, more specifically, their role as plant pathogens, your facility (referenced from your own knowledge) with the fundamental aspects of fungal biology will significantly improve your ability to conduct scientific research by positing reasonable and testable hypotheses. I also think you will find the remarkable diversity of form and function in the Fungi fascinating.

Seminar (Theoretical): The focus of this class will be on fungal diversity. As such, the primary goal of the "seminar" section of this course will be to cover theoretical aspects of fungal evolution by reading modern research papers and reviews of fungal diversity, systematics, , and population biology. A strong theoretical background in mycology will improve your ability to analyze data, interpret results, solve problems, and make significant contributions to the field.

Lab (Practical): The lab section of this course will focus on the practical aspects of systematic mycology. The primary goal of the lab (supplemented by some seminar hours) will be to build your skills in collecting, identifying, and placing the fungi you collect into a phylogenetic context. This will require developing skills in field collection, microscopy, and molecular data analysis. The mission of this course is to provide an opportunity for you to develop the skills (and confidence) to identify the fungi that you collect and place them in a broader phylogenetic context.

COURSE OUTLINE (Subject to change)

Week 1 Introductions, Syllabus, Teaching Philosophy, Assessment Quiz (8/27) Week 2 Seminar discussion: Rossman & Palm; Blackwell (2011) (9/3) Lab: Mycological toolbox: Microscopy, Collecting, Resources (Literature, Herbaria, People). Lecture: Introduction to fungi; fungal phylogenetics; , Ustilagomycotina: Ustilagomycetes (Ustilaginales), (Exobasidiales, Tilletiales); Basidiomycota, : (Septobasidiales, Helicobasidiales, Pucciniales); (Microbotryales); Week 3 Seminar discussion: Schulz & Boyle (9/10) Lab: Ustilagomycotina; Pucciniomycotina Lecture: Basidiomycota, : “” – Tremellomycetes (), (Dacrymycetales), (Auriculariales). Week 4 WORK ON COLLECTIONS! (9/17) Week 5 Seminar discussion: (9/24) Lab: “Heterobasidiomycetes” Lecture: Basidiomycota, Agaricomycotina: “Homobasidiomycetes” – Phallomycetidae (“Gomphoid-Phalloid”), (“Cantharelloid”), Hymenochaetales (“Hymenochaetoid”), Russulales (“Russuloid”) Week 6 Seminar Discussion: (10/01) Lab: “Homobasidiomycetes” Group 1 Lecture: Basidiomycota, Agaricomycotina: “Homobasidiomycetes” – Thelephorales, Boletales, Polyporales, Agaricales Week 7: Seminar Discussion: (10/8) Lab: “Homobasidiomycetes” Group 2 Lecture: , : Taphrinomycetes, Neolectomycetes; Ascomycota, : ; Ascomycota, (Pezizales, Orbiliales) Week 8: Seminar Discussion: (10/15) Lab: Taphrinomycotina; Saccharomycotina, Pezizales, Orbiliales Lecture: Ascomycota, Pezizomycotina, Week 9: Seminar Discussion: (10/22) Lab: Sordariomycetes Lecture: Ascomycota, Pezizomycotina, Week 10: Seminar Discussion: (10/29) Lab: Leotiomycetes Lecture: Ascomycota, Pezizomycotina, , Week 11: Seminar Discussion: (11/5) Lab: Eurotiomycetes Lecture: Ascomycota, Pezizomycotina, Week 12: Seminar Discussion: (11/12) Lecture: , Lab: Dothideomycetes Week 13: Seminar Discussion: (11/19) Lab: Chytridiomycota, Zygomycota Week 14: WORK ON COLLECTIONS! (11/26) Week 15: Seminar Discussion: (12/2) Lecture: Oomycota Lab: Oomycota Week 16: Open (12/9)

Seminar Readings: You and everyone else will benefit if you are prepared for discussion of the publications listed below on the appropriate date. It is my hope (interpret as expectation) that the reading will provoke thoughtful conversation.

Week 2: Systematics of Plant Pathogenic Fungi: Why It Matters Amy Y. Rossman, Mary E. Palm-Hernández http://nt.ars-grin.gov/pdfs/PDIS-92-10-1376.pdf

The Fungi: 1, 2, 3 … 5.1 million ? Meredith Blackwell American Journal of Botany 98(3): 426–438. 2011.

Week 3: The endophytic continuum. Mycol Res. 2005 Jun;109(Pt 6):661-86. Schulz B, Boyle C.

Week 4: Phylogenetic evidence of host-specific cryptic species in the anther smut Evolution 61(1):15-26, 2007 Le Gac, Hood, Fournier, and Giraud

Week 5: Asian origin and rapid global spread of the destructive dry rot fungus Serpula lacrymans Molecular Ecology 16, 3350-3360, 2007 Kauserud et al.

We will transition to using the seminar hour for computational work and phylogenetic data analysis after week five.

Fungal Wiki: You are expected to research the reproductive biology, ecology, and systematics of any group of fungi and publish your research as a wiki page. “Group” is defined as any lineage between family and species. Include a discussion of the taxonomic history (including distinguishing morphological features, important developments in classification, phylogenetic affinities, and the state of modern phylogenetic research), ecology (host and geographic distribution, habitat preferences, etc), and reproductive biology (modes of asexual and sexual reproduction, means of dispersal). You will turn this in to me as a word document.

Collections: You are expected to choose a host plant of interest from which you will isolate and identify (preferably to or species) 10 unique species. If you isolate two species from the same genus, you are expected to identify the isolates to species. Please choose a host species that is not a major economic crop (corn, soybean, cotton, etc.). The following items are required to accompany your collections: 1. Prepare a voucher specimen of the host species that is suitable for deposition in an herbarium. 2. Isolate or collect (pathogenic, endophytic, epiphytic, saprophytic, mycorrhizal, etc.) fungi from the host of interest. Those fungi that are cultured must be isolated into pure culture. I recommend maintaining them for the semester on a low nutrient medium such as CMA (corn meal agar). Two of the ten collections must be pure sporulating cultures. All collections (other than cultures) must be dried and presented at the end of the semester with your field and lab notebooks. 3. Maintain a field notebook of your collections and assign collection numbers to each collection. 4. Identify each collection as accurately as possible. 5. Provide a detailed description of five of your collections in your lab notebook. Please include the collection number that corresponds to your field notebook. Provide a detailed description, including illustrations (can be photomicrographs), of the specimen suitable to convince me that it is accurately identified. 6. Prepare permanent slides of two sporulating cultures suitable for deposition to the slide collection.

Lab Notebook: Your participation in lab will be gauged in part by your lab notebook. Maintain an organized lab notebook with detailed notes and illustrations of what you see in lab. There are no formal requirements for the notebook, but you should view it as a resource for your future mycological pursuits.