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Sarah writes: The 32nd Fungal Genetics Conference, held at the Asilomar Conference grounds in Pacific Grove California in March 2024, welcomed almost 850 scientists from 35 different countries. The main meeting was formed of 4 morning plenary sessions – on functional genomics; fungal metabolism; pathogens and symbionts and fungi in the biosphere; followed by afternoon workshops and network gatherings and then 7 themed sessions, and with poster presentations each night up until 10 pm. This formal meeting was preceded by several satellite workshops on topics ranging from sessions on Aspergillus, Magnaporthe, Fusarium, basal fungi and Dothideomycetes. Sarah attended 2 such sessions, hosted by Canadian Institute for Advanced Research (CIFAR) – on animal and plant-fungal interactions, basal fungi and fungal biology.
Despite the intensity of the programme there was still time to imbibe the glories of an unusually green Californian spring and a dip in the cool sea. The conference site was designed by Julia Morgan and built in the early 1900s, originally as a retreat for the Young Women’s Christian Association. Eleven of the original arts and crafts style buildings remain, joined by similar “in style” erections – all nestled along the Pacific Grove coastline. A few footsteps along the boardwalk from the lectures halls finds delegates amongst the sandy dunes and on the beach. Hardly surprising then that this conference is always a “sell out” shortly after registration opens. It is the most magical of places for inspiring new science, catalysing creative conversations, finding new friends and for meeting old academic colleagues.
Fungi have recently captured the public’s imagination – with such grim stories as the TV series ‘The Last of Us’ and with the cleverly-crafted writings of Merlin Sheldrake in his book ‘Entangled Life’. But we at Asilomar are already ensnared by our fascination for fungi. Whilst we realise that we have named a mere 1% of fungi in the biosphere we are finally beginning to understand their incredible diversity thanks to efforts such as those described by Igor Grigoriev (DOE Joint Genome Institute) and Richard Hamelin (UBC), who showed us that machine learning enables us to recognise the genomic signatures of different lifestyles and fungal traits in plant pathogens. So AI looms large, but so too does one more old fashioned technique, enjoying a renaissance – that of CHEF analysis of fungal chromosomes by pulsed-field gel electrophoresis. Several talks embraced this 1980s technology – Anna Selmecki (Minnesota) describing the architecture of antifungal resistance in Candida, Reem Aboukhaddour (Agri-Food Canada) pinpointing the chromosomal location of effectors in the tan spot fungus and Thorsten Langer (Max Planck, Tuebingen) and colleagues revealing that the rice blast fungus horizontally transfers mini-chromosomes between fungal lineages. There was also a series of clever talks about transposons, not least the starship family – a class of snip and paste transposable elements found across the Kingdom, hallmark signatures which have likely shaped fungal genomes for millennia.
With total and unashamed bias, I finish my thoughts with two of the 5 superb talks given in the final plenary session, which I chaired, with Reinhardt Fisher, that is ‘Fungi in the Biosphere’. Firstly, with the sheer beauty of the sequence of images, accompanied by Vivaldi ‘s Four Seasons (winter) shown by Yen-Ping Hseuh (Academia Sinica) in her talk about nematode trapping fungi, and secondly, with the exciting possibility that Marc Orbach (Arizona) has led a team to develop a live attenuated fungal vaccine against Coccidioidomycosis / Valley fever.
Hannah writes: The 32nd Fungal Genetics conference in Asilomar, #Fungal24, showcased the diversity and depth of current fungal research, with new insights and explorations of tools (new and ‘old’) to tackle challenges in understanding fungal biology and the implications for agriculture, ecology, and medicine. Choosing my top three talks was challenging: many inspired curiosity, joy and fresh ideas. Just some of the names I managed to see (not including the wonderful poster sessions!), Asiya Gusa, Cristina Barragan, Nichola Hawkins, Jie Gao, Axel Brakhage, Anna Selmecki, Megan McDonald, Daniel Croll, George Lund, Anton Kraege, Barbara Valent, Johanna Rhodes, Alexandra Dellaire, Abigail LaBella, Arnold Driessen, Michael Habig, Charissa de Bekker and Yen-Ping Hsueh. But as I had to pick three.
Yukiyo Sato from Bart Thomma’s group at the Institute for Plant Sciences, University of Cologne, presented work on chromosomal engineering in the plant pathogenic fungus Verticillium dahliae. Their research delved into adaptive genomic regions (AGRs), which are dynamic compartments of the genome characterised by extensive rearrangements, such as segmental duplications and reciprocal gene losses. These AGRs are enriched with in planta induced virulence genes, active transposable elements, histone modification markers such as H3K27me3, and structural variation. Intriguingly, despite their scattered presence throughout the genome, these AGRs have been observed to cluster together within nuclei physically. Sato’s work probes the intriguing question of whether AGRs are the cause or consequence of chromosomal rearrangements. Using a CRISPR-Cas9 system, they successfully induced a reciprocal chromosomal translocation of a substantial AGR cluster with a core genomic region across two chromosomes. While no differing growth phenotypes were observed, an RNA-seq analysis of the translocation mutant revealed a subtle shift. Approximately 2% of genes exhibited differential expression relative to the wild-type, underscoring the influence of chromosomal translocation on the fungal transcriptome. I was excited by the potential of these experiments to explore causal relationships between chromosomal structure and fungal pathogenicity.
Cécile Lorrain from Bruce McDonald’s group at ETH Zurich presented a study on the host adaptation mechanisms of the wheat fungal pathogen Zymoseptoria tritici. They identified genomic traits associated with host adaptation through a novel approach to interrogating genome-wide association studies (GWAS). The data that went into the analysis included whole-genome sequencing data from 830 virulent Z. tritici strains isolated across 12 wheat cultivars of varying susceptibility. Their approach selected a group of virulent strains to an initial focal wheat cultivar, then compared those against random sub-samples of strains isolated from different cultivars and using a bootstrapping method. Lorrain showed proof of concept for the approach, re-finding Avr3D1 in their analysis, and whilst not ready to go into detail, they indicated a diversity of gene functions from predicted effector candidates to transcription factors being identified. I was most excited by the use of natural infection data, and how this approach avoided time-intensive phenotypic screening of each individual isolate against multiple host cultivars!
During the penultimate concurrent conference session, I swapped into the ‘Fungi at the cutting edge’ session with an interest in learning more about microfluidic devices, but I was particularly impressed by the last presentation in the session. Tomás Rush from the Bioscience Division at the Oak Ridge National Laboratory delivered a talk on rapid ionomic profiling using laser-induced breakdown spectroscopy (LIBS). They conducted this ionomic profiling of two genetically distinct fungi grown on defined (known compositions and concentrations) and undefined substrate media to identify and correlate trace elements present within an organism. In Hyaloscypha finlandica and Mucor hiemalis, the study demonstrated the necessity of elements like carbon, zinc, phosphorus, manganese, and magnesium; this aligns with these micronutrients’ well-established roles in critical biological functions of fungi. However, this study also identified some differences in ionomic profiles of these two fungi. For example, H. finlandia also exhibited a strong positive correlation toward sodium, indicating a reliance on sodium in this fungus, unlike M. hiemalis, which did not. Although some of the outcomes of this study could have been predicted, it interested me especially as we categorise fungal plant pathogen lifestyles by their nutrient acquisition strategies (biotrophy, necrotrophy, etc.). Reading additional related research, I found that x-ray fluorescence microscopy has been used to identify spatial and temporal in situ elemental differences between Pyrenophora tritici-repentis infected symptomatic, asymptomatic, and healthy wheat leaf tissue, highlighting some further possibilities of such techniques.
As I made my way to join with friends (new and ‘old’), I considered the parallels of LIBs to the astronomical spectroscopy that detailed the composition of distant stars. My imagination wove sessions together: fungi growing upon microfluidic chips, glowing with fluorescent tags, their cellular processes synced to circadian clocks, engaging in silent battles with secondary metabolites, interrupted by flashes of laser beams and all the while, starship transposons are making their genomic voyages. Then something far less cosmic dawned on me – I had left my coat at a previous session, making #Fungal24 attendees from Rothamsted Research 2 for 3 on misplaced coats.
We both wish to thank the BSPP committee for their generous sponsorship for us to attend this truly inspiring conference.
Hannah Blyth, Rothamsted Research
Sarah Gurr, University of Exeter
