32nd Fungal Genetics Conference
32nd Fungal Genetics Conference
The Perkins/Metzenberg Lecture is a thought-provoking perspective given by a leader in the field of fungal genetics that often includes an historical perspective, thoughts for the future, and some humor. We are pleased to announce the 2024 Perkins/Metzenberg Lecture will be given by N. Louise Glass, University of California at Berkeley.
N. Louise Glass
N. Louise Glass is an Emeritus Professor in the Plant and Microbial Biology Department at the University of California, Berkeley. Her research interests include applying systems biology approaches to dissect nutrient signaling and plant cell wall deconstruction by fungi and defining molecular mechanisms associated with cooperative (cell/hyphal fusion) and antagonistic (allorecognition and fungal innate immunity) interactions between fungi. More recently, Glass has been involved in the development of functional genomics approaches for non-model fungi.
Previous Perkins/Metzenberg Lectures:
2022 – Gillian Turgeon, Cornell University
2019 – John Taylor, University of California, Berkeley
2017 – Jay Dunlap, Geisel School of Medicine, Dartmouth University
2015 – Michael J. Hynes, University of Melbourne
2013 – Regine Kahmann, Max Planck Institute for Terrestrial Microbiology
2011 – Salomon Barnicki-Garcia, Cicese
2009 – Claudio Scazzocchio, University of Paris
2007 – June Kwon Chung, National Institutes of Health
2005 – Joan Bennett, Tulane University
2003 – Hans VanEtten, University of Arizona
2001 – Ronald Morris, Rutgers University
1999 – Rowland Davis, University of CA, Irvine
1997 – Lorna Casselton, University of Oxford
1995 – Robert Metzenberg, University of Wisconsin, Madison
1993 – Cardy Raper, University of Vermont
1991 – David Perkins, Stanford University
1989 – Charles Yanofsky, Stanford University
Functional genomics illuminates foundational biology and evolution
Melania Figueroa
Victoriano Garre
Thorsten Langner
Anna Selmecki
Multilevel regulatory circuits to understand fungal metabolism
Zachary Lewis
Jolanda van Munster
Chris Koon Ho Wong
Bing Zhai
Underneath, within, and around: pathogens and symbionts
Andrea Genre
Ksenia Krasileva
Marcio Rodrigues
Barbara Valent
Interactions of fungi with the biosphere
Mukesh Dubey
Charissa de Bekker
Yen-Ping Hsueh
Marc Orbach
Genetic control of primary and secondary metabolism, Chairs: Maria Cristina Stroe (Germany), Richard Wilson (US)
Fungal growth and development are mediated by primary metabolism, which also provides building blocks for chemically diverse secondary metabolites with ecological roles in inter-organismal communication, competition and virulence. However, although primary and secondary metabolism and underlying resource-allocation strategies are exquisitely regulated in response to available nutrients at the transcriptional, translational and epigenetic level, the molecular details are often poorly understood. In this session, we aim to illuminate the current state of knowledge on various aspects of primary and secondary metabolic control in diverse fungal systems with a view to tackling unanswered questions in understanding how primary and secondary metabolism are integrated and how these fungal processes might be subverted to our benefit.
Chromatin and chromosome biology, Chairs: Slavica Janevska (Germany), Mareike Moeller (Australia)
Fungal genomes are highly diverse, even between isolates of the same species. Variable regions are often associated with specific chromatin modifications and linked to adaptive chromosome regions which may offer a selective advantage to the fungus under certain conditions. Chromatin modifications are traditionally linked to gene expression dynamics, but more recently, connections between genome organization and evolution and the presence of chromatin environments have become the focus of many studies. We are intrigued by the diverse roles chromatin plays in fungal species, ranging from transcriptional control of pathogenicity-related genes and transposons to important determinants of mutation frequency and genome stability. In this session, we aim to bring together the latest genome and chromatin research on different fungal species to explore the remarkable diversity of fungal chromatin and chromosome biology.
Phase separation and sequestration, Chairs: Amy Gladfelter (US), Yansong Miao (Singapore)
Macromolecular condensates, comprising nucleic acids, proteins, and lipids, dynamically assemble in response to physiological or stress conditions. These assemblies underlie diverse biological processes, including development, stress adaptation, and host infection. The fundamental mechanisms governing these functions arise from phase separation, which can either activate or sequester participating biomolecules. This session invites submissions exploring all facets of macromolecular condensation in fungal systems, encompassing physiology, evolution, and pathology. We particularly encourage interdisciplinary contributions that offer a comprehensive understanding of phase separation processes and functions.
RNA biology, Chairs: Anita Sil (US), Qiang Cai (China)
Since the dawn of life, RNA has played a central role in cellular processes, including decoding genomes, regulating gene expression, mediating intermolecular interactions, and catalyzing chemical reactions. The RNA-mediated gene regulation network in fungi is tightly controlled at multiple levels. Some molecular mechanisms are conserved among eukaryotes, while others have evolved differently. In this session, we invite the submission of topics dealing with the fungal RNA machinery and RNA-dependent processes, including transcription & translation, non-coding and regulatory RNAs, small RNA-mediated gene silencing, RNA trafficking, RNA metabolism, bioinformatics tools for RNA analysis, and other topics relevant to RNA biology.
Connections between light, clocks, and stress, Chairs: Jennifer Hurley (US), Monika Schmoll (Austria)
The rotation of the Earth brings about substantial changes in environmental conditions for all organisms, including fungi. Light represents the primary environmental cue from this rotation and can influence the stress response via several mechanisms, often through the regulation of fungal primary and secondary metabolism. Adaptation to, and anticipation of environmental cues throughout evolution has increased species fitness and competitive success. In fungi, the cellular circadian clock assumes the task of coordinating a complex network of gene regulation, posttranscriptional regulation, and modulations in protein modification to respond to light conditions. In this session we aim to bring together different views on the complex interrelationships of light with clocks and stress responses, from molecular regulation mechanisms to intriguing physiological and evolutionary effects in diverse fungi.
Signaling in the gas phase, Chairs: Joan Bennett (US), David Ezra (Israel)
Volatile organic compounds (VOCs) are a class of carbon-based compounds characterized by their low molecular mass and high volatility. Because they readily vaporize under standard atmospheric conditions, biogenic VOCs are useful signaling molecules in non-aqueous environments. Fungal volatiles are known by their distinctive odors. Moreover, they exhibit a diverse array of biological functions, encompassing bio-stimulation, self-inhibition, antibiotic properties, insect attraction or repulsion, abiotic tolerance and biofertilization, among others. It is postulated that fungal VOCs assume a pivotal role in mediating intraspecific and interspecific communication between fungi and other organisms. Within the context of this session, our objective is to examine the multifaceted roles of fungal VOCs and their implications in the life cycle of fungi, as well as their interactions with other cohabiting organisms.
Polarized growth: 100 years with a Spitzenkoerper, Chairs: Meritxell Riquelme (Mexico), Juergen Wendland (Germany)
The Spitzenkörper is a structure found at the apex of fungal hyphae and serves as organizing center for hyphal growth and morphogenesis. The Spitzenkörper was first described by Brunswik in 1924, who stained the vesicles marking the Spitzenkörper with iron-hematoxylin, and it was studied by Girbardt in the 1950s by phase contrast microscopy. This session aims to reflect on the historical contributions that illustrate our understanding of the vesicle supply center and dissect the Spitzenkörper on the genetic and cell biological level by looking at genes involved in secretion, endocytosis, and genes required for the establishment and maintenance of polarized growth in different systems.
Morphogenesis at multiple scales, Chairs: Rob Arkowitz (France), Nancy Keller (US)
In response to a changing environment, fungi change their shapes to optimize nutrient acquisition, reproduction, and responses to biotic or abiotic signals. During these transitions, dramatic cellular and subcellular reorganization can occur, that ultimately are critical for specialized structures and functions. Furthermore, changes at the multicellular level, i.e. in the organization of mycelial networks, play an important role in adapting to new environments. In this session we welcome submissions addressing fungal morphogenesis in diverse environments over a range of size scales from the subcellular to the multicellular.
Cytoskeleton and intracellular transport, Chairs: Xin Xiang (US), Rosa Mourino Perez (Mexico)
Hyphal growth of filamentous fungi is highly polarized, and it involves various cytoskeletal components such as microtubules, actin, and septins. In elongated hyphae, organelles, vesicles, and their hitchhiking cargoes are distributed via directional transport mediated by molecular motors. In this session, we aim to cover the contributions of various cytoskeletal components to hyphal growth as well as mechanisms of directional transport in elongated hyphae.
Multicellular development, Chairs: Ines Teichert (Germany), Jan Dijksterhuis (The Netherlands)
Fungal cells are connected into a mycelium which is multicellular in nature. The iconic network picture has many variations. For example, hyphae can grow in bundles and form cords with surprising properties, and fungal cells can grow in meristematic structures that withstand extreme conditions. They can interact with plant cells as in lichen and mycorrhizal associations. Moreover, they interact and develop into a wide variation of fruiting bodies in which the hallmark of fungi, the hypha can still be recognized. This session highlights numerous aspects of fungal multicellularity and includes topics such as the genetic regulation of multicellular development, evolution of multicellularity, modelling of multicellular development, differentiation occurring in yeast colonies and liquid cultures, and the formation of fruiting bodies and overwintering structures.
Beyond the Dikarya: Studies on basal fungi, Chairs: Lillian Fritz-Laylin (US), Kerstin Voigt (Germany)
This session is dedicated to shedding light on a less-explored group of fungi, often called “basal fungi”. Once at the forefront of fungal biology and then almost forgotten, basal fungi are being vindicated for their untapped potential for understanding fungal diversity, evolution, and ecology. This session will showcase the immense diversity within basal fungi. We welcome a wide range of topics, encompassing aquatic and terrestrial fungi, with a specific focus on molecular ecology, phylogeny, evolution, genome and cell biology, as well as practical applications. Of particular interest are fungi thriving in challenging environments, such as anaerobic habitats and those in symbiotic interactions with prokaryotic and eukaryotic hosts. We extend a special invitation for submissions related to developing genetic tools that empower researchers to dissect gene functionality in these remarkable fungi.
Mobile elements and dynamic genomes, Chairs: Aaron Vogan (Sweden), Emile Gluck-Thaler (Switzerland)
Advances in sequencing breadth and quality are revealing new dimensions of diversity within fungal genomes: just as fungi often colonize plants and animals, fungal genomes are themselves colonized by multitudes of mobile elements, DNA-based entities that replicate semi-independently of fungal genomes yet are fully nested within them. Once thought to be little more than “junk” DNA, mobile elements and repetitive elements are increasingly shown to have unexpected and important consequences for fungal genome evolution and function. Fungi harbor mobile elements ranging from several hundred basepairs to massive genomic islands or entire accessory chromosomes, with new classes of elements being discovered at breathtaking speed. This session will explore how these elements shape fungal physiology, ecology, and evolution by leveraging diverse perspectives and approaches ranging from the molecular to the computational.
Horizontal gene transfer, meiotic drive, and related phenomena, Chairs Like Fokkens (The Netherlands), SaraH Zanders (US)
In most cases, heredity in eukaryotes strictly follows a set of rules. These rules dictate that organisms inherit all their genes from their parent or parents. The rules also specify that during sexual reproduction, the transmission of alleles into offspring is balanced. Specifically, a heterozygote carrying two distinct alleles (e.g., A/a) will pass each allele to half their progeny. This session, however, is about cases where those rules of heredity are broken. Topics will include mechanisms of horizontal transfer of genes or chromosomes between organisms, and meiotic drivers, which are genetic parasites that bias sexual reproduction to promote their own transmission into offspring.
Experimental evolution with fungi, Chairs: Shay Covo (Israel), Robb Cramer (US)
Fungi affect ecosystem, plant, animal, and human health in many ways. They are important emerging pathogens, but also form beneficial symbioses, e.g. mycorrhiza and plants. Experimental evolution approaches have emerged as a powerful tool to decipher the evolution and genetics of complex fungal phenotypes. Using this approach, the role of unanticipated genes and pathways in pathogenicity, fungicide resistance, precision fermentation, and basic fungal biology have been discovered. Experimental evolution not only provides input into the genes involved in a given phenotype, but also about the order and mechanisms of the events needed to bring cells from one state to another and the different trajectories that can be taken. We will discuss how experimental evolution can teach us how fungi acquire complex phenotypes in our dynamic world.
Evolving metabolomes by divergent genome architectures, Chairs: Milton Drott (US), Tomas Rush (US)
The advent of the -omics era has revealed that the evolution of fungal metabolites is impacted by interactions with gene products encoded in the same genome and by the different ecologies enabled by differences in fungal genomes. We are intrigued at how genetic, metabolic, and ecological contexts encoded within genomes result in ‘architectures’ that shape the evolution of metabolites. Gene content does not always result in the same ecological function or end product. Different architectures can manifest as epistatic interactions between genes (e.g., biosynthetic pathways), regulatory interactions, chemical interactions, and ecology-dependent functionalities, allowing the opportunity to explore the consequences of genes included in genomes with a different evolutionary history. This session invites submissions exploring the mechanisms by which genomic architectures diverge and what the consequences of this divergence are on metabolic diversity and metabolite-mediated ecologies.
Fungi in microbial ecosystems, Chairs: Jessie Uehling (US), Bart Thomma (Germany)
Fungi are present in complex microbial communities and ecosystems where they coexist and interact with other microbes, including bacteria and viruses, in addition to more complex hosts such as plants and animals. The study of interactions between microbes and their eukaryotic hosts has been coined “metaorganismal” research. In addition, the existence of close fungal relatives across environmental gradients and within a diversity of niches suggests the environment also plays a role in shaping the evolutionary trajectories of fungi and metaorganisms. How fungi and metaorganisms impact microbial ecosystems has become a recent focus. In this session we will address mechanistic fungal symbiotic questions, fungal bacterial or viral interactions, fungal metaorganismal research, fungal innate immunity, fungal community ecology, fungal diversity, and evolution of fungi in microbial ecosystems.
Multi-trophic fungal interactions: integrating chemical, molecular, and metagenomic approaches, Chairs: Kai Heimel (Germany), Jeffrey A. Rollins (US)
A burgeoning area in fungal biology is focused on understanding how fungi communicate and interact with other organisms. Contemporary findings utilizing chemical, molecular, and metagenomic tools have revealed the identities of a growing variety of small molecules, including secreted peptides, volatile organic compounds and secondary metabolites that are involved in interspecies communications that modulate complex biological processes. For example, oxylipins can influence fungal gene expression and bacterial fitness, mycotoxins can inhibit competing microbes at the infection site and exert symptoms on the host, endophytic fungi can impact plant pathogens by modulating basic processes such as metabolite efflux, and pathogenic fungi secrete small protein effectors to modulate host defense and promote virulence. This session will highlight scientific questions involving model and non-model fungi expressing variation in symbiosis and trophic interactions with two or more partners across kingdoms.
Extremophilic and anaerobic fungi, Chairs: Michelle O’Malley (US), Cene Gostinčar (Slovenia)
Fungi inhabit almost all environments on our planet, even those in which most organisms cannot survive, let alone thrive. In their adaptations to extremes, they can rival and, in some cases, surpass even prokaryotes, with the exception of high temperatures. Certain species of fungi colonize extremely cold, salty, dry, acidic, alkaline, and other environments, while other species can survive without oxygen. This session will focus on fungi from extreme and anaerobic environments, with particular attention to their ecology, adaptations, and numerous biotechnological applications.
Diversity and biotechnology of marine and estuarine fungi, Chairs: Frank Kempken (Germany), Cassandra Ettinger (US)
Marine and estuarine fungi, which were once largely ignored, are now an exciting area of fungal research. It is clear that fungi play important and underappreciated roles in carbohydrate degradation, nutrient cycling and host health in these niches, and they have been shown to be highly adaptable and capable of producing a plethora of novel secondary metabolites, many of which may be highly useful in biotechnology. However, we are currently limited by our rudimentary understanding of the diversity, behavior and function of marine and estuarine fungi, as well as by a lack of robust tools to easily manipulate and characterize their secondary metabolites. In this session, we address all aspects of marine and estuarine fungi, ranging from surveys of diversity to biotechnological applications, and encourage submissions which integrate across multiple disciplines.
Mycoviruses, Chairs: Ioly Kotta-Loizou (UK), Marc Meneghini (Canada)
Fungi are infected by mycoviruses that employ novel transmission and replication strategies. Although largely asymptomatic on their fungal host, mycovirus infection is well-known to positively or negatively affect the virulence of fungal species that are pathogens of plants or animals. In recent years, the use of high-throughput RNA sequencing has greatly accelerated mycovirus discovery, and the field is rapidly growing. We will discuss topics including mycovirus discovery and characterization, replication and infectivity, impact on host cell fitness and pathogenicity, and fungal antiviral systems.
Understanding fungal pathogenesis by genomics, Chairs: Daniel Croll (Switzerland), Aleeza Gerstein (Canada)
Genomics opens the door to studying fungal pathogenesis in new ways. In this session we will examine pathogenesis from all angles – agricultural, forestry, medical – and ask questions from ecology, evolutionary, and functional perspectives. We welcome discussion of innovative applications of genomics technology including the development of new methods or analysis techniques.
Biofilms, biocontrol, and disease prevention by genome engineering, Chairs: Joanna Tannous (US), Federico Lopez (Spain)
Biofilms are the main growth lifestyle of many opportunistic fungal pathogens and play key roles in the emergence of fungal resistance to antimycotics. Hence, there is an urgent need for novel practices to prevent fungal resistance and ensure effective disease management. There is a worldwide tendency to lessening the use of chemically synthesized fungicides, while biocontrol strategies and genome engineering tools are emerging as new approaches for fungal disease management. This session will help to unravel the cellular and molecular mechanisms that enable pathogenic fungi to generate biofilms and develop resistance, covering the current state of the art on the multiple interactions between fungal pathogens, biocontrol agents (BCAs) and their hosts. Lastly, this session will include recent advances in fungal genome engineering to control fungal infections and to the development of novel genetic diagnostic and therapeutic tools of fungal diseases.
New technologies to understand and control antifungal resistance, Chairs: Christian Landry (Canada), Sabine Fillinger (France)
There is only a handful of antifungal molecules regularly used in clinics and agriculture; resistance to those can evolve during treatment or even segregate among naturally occurring populations of opportunistic fungi. In a context where new drugs are only slowly being developed, and drug targets are limited, it is imperative to develop approaches and strategies to better understand resistance mechanisms. This session will cover new and innovative approaches to understanding how resistance to antifungals and fungicides evolve and which methods can be applied to delay or control resistance evolution.
Mechanisms of resistance to fungicides, Chairs: Matthew Fisher (UK), Daniel Santos (Brazil)
Fungi play a pivotal role in agriculture and health, on one hand affecting crop yields and food security while on the other posing a substantial threat to human health. However, the widening emergence of resistance to antifungal chemicals is raising significant concerns. Understanding the intricate mechanisms by which fungi develop resistance is important as this knowledge not only impacts health and agriculture, but also has important one-health implications owing to the development of cross-resistance in pathogens when agricultural and clinical antifungal agents share the same mode of action. This session serves as a platform to share cutting-edge research aimed at addressing the growing global issue of antifungal resistance.
Fermentation, biorenewables, and the built environment, Chairs: Han Woesten (The Netherlands), Roberto Nascimento Silva (Brazil)
Fungi can be highly instrumental in the transition to a sustainable economy. They can, for instance, be used to replace non-sustainable foods, and to produce biofuels, bioplastic building blocks, and mycelium materials. Moreover, fungi can be used to change properties of materials like wood or can be used in bioremediation. This session will report on the current state of the use of fungi in the transition to a sustainable economy.
Fungi for sustainable food production, Chairs: Maiko Umemura (Japan), Debbie Yaver (US)
To meet the protein needs of a growing human population, ~10 billion by 2050, the demand for meat is projected to double, while land, water, and other natural resources cannot. In addition, animal agriculture is responsible for approximately 20 percent of the global greenhouse gas emissions every year. All this points to a need for developing alternative protein sources to sustainably feed the world. Along with alternative proteins, other technology such as the production of sustainable fats and oils will be important to enable products that are nutritious and delicious. Fungi have a long history of use in the fermentation industry for food use. This session will focus on the current state of traditional uses of fungi in food as well as uses to produce non-animal derived food such as alternative meat, non-dairy products and other alternative ingredients.
Machine Learning in Fungal Genetics, Chairs: Abbe (Abigail) LaBella (US), Benjamin Schwessinger (Australia)
Studies of fungal genomics, ecology, and phenotypes now produce “big data.” The concerted efforts of many groups have produced datasets ranging from thousands of genomes to global taxonomic surveys driven by citizen science. The size, variety, and complexity of these datasets make them particularly ripe for interrogation with machine learning methods. Moreover, machine learning methods are now accessible to researchers with a wide range of computational expertise. This session highlights applications of machine learning to outstanding questions in fungal genetics. We will focus on applications of machine learning to solve “big questions” in fungal research, such as studies of fungal complex traits, pathogenesis, diversity, and ecology. We hope this session will be a starting point for fungal researchers interested in applying machine learning to their research questions.
Fungi at the cutting edge – microfluidics and other new tools, Chairs: Erin Bredeweg (US), Norio Takeshita (Japan)
The utilization of microfluidics, which allows for the artificial design and precise control of microenvironments, is uncovering novel aspects of fungal biology. Other new tools, such as Imaging MS, XRD, Raman spectroscopy, and their combined applications are promising for the advancement of basic and applied research in the field of fungal biology. This collection of new ideas and several use cases will give an opportunity to consider how microfluidics and molecular analysis technologies can be applied to synergistic research and new collaborative efforts.
