Fungal Evolution Symposium

Haeckel (1904) Kunstformen der Natur

8-9 November 2016Max Planck Institute for Evolutionary

Biology, Plön

Tuesday9:00 Introductory remarks

9:15 Jaqueline HessExamining genomic changes sustaining ecological transitions in fungi – or learning how to talk to plants

10:00 Inger SkredeThe fungus that came in from the cold: evolutionary necessities for invading buildings

10:45 Coffee break

10:15 Joana BernardesHeterozygosity influences hybrid fitness

11:35 Sundy MauriceFungi on the move: Don’t stand so close to me!

12:20 Lunch

14:45 Hanna JohannessonGenomic conflict as a driver of genome evolution: insights from the fungal spore killers

15:00 David RogersBeauty and the yeast: translational control of Saccharomyces pheromone production and mating success

15:20 Primrose BoyntonSurvival, bet-hedging, and sex: What's a spore for?

15:40 Social hike with discussion

18:30 Barbecue for all participants

Wednesday9:00 Marie Davey

Who’s driving? Host-parasite evolution in the bryophilous genus Lizonia

9:45 Chaitanya GokhaleHost-parasite coevolution in a domesticated world

10:05 Christoph EschenbrennerEvolutionary genomics and population genetic analyses of the Zymoseptoria species complex

10:25 Coffee break

11:00 Ezgi ÖzkurtGenome Evolution of the Fungal Grass Pathogen Zymoseptoria pseudotritici

11:20 Frank KempkenMarine Fungi - identification, genomics and transcriptomics

12:05 Lunch and discussion

Paid for by the workshop program of the MPI for Evolutionary Biology

Abstracts:

Examining genomic changes sustaining ecological transitions in fungi – or learning how to talk to plantsJaqueline Hess, University of Vienna

Fungi are evolutionary shape shifters, harbouring the ability to rapidly adapt to new environments. Many fungal ecotypes, for example mycorrhizal symbionts, plant and animal pathogens or finely tuned wood decayers that have shunted the need for costly enzymatic machinery have evolved repeatedly and independently across the fungal tree of life. These remarkable instances of convergent evolution suggest both, the presence of a strong intrinsic property of fungal genomes to form these reoccurring ecotypes, and the ability to reconfigure their genome content and its expression accordingly. Here, I will use two examples at different evolutionary time-scales to illustrate how various mechanisms of genome evolution have shaped genomes across such ecological transitions, and where superficially distinct ecologies may have common evolutionary starting points. Examples will include the transition from asymbiotic to ectomycorrhizal ecology in the genus Amanita and specialisation of wood decay mechanisms in the invasive brown rot fungus Serpula lacrymans, in its adaptation to the human built environment.

The fungus that came in from the cold: evolutionary necessities for invading buildingsInger Skrede, University of Oslo

Many organisms benefit from being adapted to niches shaped by human activity, and have successfully invaded human-made habitats. One such species is the dry-rot fungus Serpula lacrymans that decomposes coniferous construction wood. This species has spread from its natural high mountain habitat in Asia to houses in temperate regions worldwide. In this study we analyse which physiological and genomic features separate S. lacrymans from close relatives growing in forests, and which features that divide different S. lacrymans populations growing in houses. We demonstrate that S. lacrymans is more specialized in which wood species it prefers and is a poorer competitor than its wild relative S. himantioides, which encounters many more competitors in its natural habitat. Further, genomic mechanisms related to intracellular transport, specialized metabolism and wood decomposition mechanisms seem to have been important to shape the different Serpula species. Nevertheless, the different populations of S. lacrymans behave differently and have a different evolutionary history. Thus, in order to understand what makes a successful invader of the built environment the population history is also an important part of the puzzle. I will present recent results of these analyses.

Heterozygosity influences hybrid fitnessJoana Bernardes, MPI Plön

Domesticated yeast diploids will tend to accumulate recessive deleterious mutations, which cannot be purged from the population because they are never exposed to selection. Domesticated diploid strains are therefore expected to have numerous masked recessive deleterious alleles, consistent with the high levels of heterozygosity

previously described. Wild strains of S. cerevisiae and S. paradoxus have low levels of heterozygosity and therefore are likely to carry fewer recessive deleterious alleles. When domesticated isolates are brought to the laboratory, the heterozygosity is eliminated, because most studies are done with haploid strains, or with diploid strains that were derived from a single spore (autodiplodized or selfed), so the resulting diploid is completely homozygous, masking the true heterozygous nature of the isolates. This loss of heterozygosity exposes the accumulated recessive deleterious alleles, resulting in low fitness. When two domesticated strains are crossed together, much of the heterozygosity is restored and the fitness of the resulting diploid will increase relative to the homozygous “parent”. We argue if the hybrid fitness was compared to that of the original heterozygous diploid parents, the fitness difference would be much reduced if there is any. On the other hand, when wild isolates are made homozygous, there will be few recessive alleles exposed. Consequently, we expect little fitness differences between the wild diploid strains and their homozygous derivatives, so there would be no fitness advantage of hybrid when compared to either parent.

Fungi on the move: Don’t stand so close to me!Sundy Maurice, University of Oslo

Dispersal is key process that underpins ecological genetics, it plays an important role in population dynamics and consequently in the maintenance of species diversity and genetic variation. Fungi producing large quantities of spores are supposed to have greater capacity for dispersal and hence giving rise to large and widespread populations. Despite this high potential to disperse, macrofungi, known to produce billions of spores a day, are threatened in many European forests, hence resulting in an increase in awareness and establishment of Red-Lists of threatened fungal species. Forest loss and habitat fragmentation is one of the main causes of biodiversity loss. In Fennoscandia, considerable loss and fragmentation of natural forests have taken place during the last centuries due to intensive forest management and short rotation times, together combined with a substantial reduction in the amount of dead wood on ground. The aim of my research is to reveal how the genetic variation within species has been affected by habitat fragmentation. Given the diversity and ecological importance of fungi, there is however a lack of population genetic research. The main reason for this can be explained by the cryptic nature of fungi and the difficulty of delimiting the individuality boundaries. In this study, the ability of restriction-site associated DNA (RAD) sequencing to generate SNPs in polypore species was examined. Different trends of the genetic diversity among the species are observed. The data were analyzed using tests of Hardy-Weinburg equilibrium, population genetic statistics and population structure were inferred using the program fineRADstructure. Differences in allelic frequencies and populations sizes exhibited among species suggest that the abilities to persist as an isolated population could be threatened while species presenting larger population size may present higher fitness. This study brings insights about genetic variation of fungi at a finer geographic scale and indicates the potential to address population genetics and evolutionary questions at broader geographic scales.

Genomic conflict as a driver of genome evolution: insights from the fungal spore killersHanna Johannesson, Uppsala University

Conflicts caused by selfish genetic elements is expected to be a driving force for evolutionary innovation, and hence, of fundamental importance for all aspects of evolution. In my research group, we use the filamentous ascomycete Neurospora as a study system of the impact on meiotic drive on genome evolution. In this genus, the meiotic drive element Spore killer is found. In sexual crosses between strains carrying a Spore killer element and wild-type strains, half of the spores will die and all the surviving spores will carry the killer element. We have investigated direct and indirect effects of carrying the element and preliminary data suggest that it is reducing the fitness of the carrier. Furthermore, we have undertaken a genomic approach to identify the killer elements and to analyze their effect on genome architecture. This data has revealed a complex pattern of inversions, insertions and deletions that may play an essential role in maintaining the region of suppressed recombination between the killer elements and their resistance factors, and in explaining the birth and death of new Spore killers over evolutionary time. Taken in combination, results emerging from this project suggest that meiotic drive has evolved multiple times independently in Neurospora and in spite of host genome defense, it has had a profound effect of genomic architecture in this genus.

Beauty and the yeast: translational control of Saccharomyces pheromone production and mating successDavid Rogers, Ellen McConnell, Duncan Greig, MPI Plön

Many complex behaviours, including those of unicellular organisms, are regulated by peptides derived from polyproteins: large prohormones that are cleaved to release multiple bioactive peptides. Despite their importance, very little is known about polyprotein evolution. The MFα1 gene of the baker's yeast Saccharomyces cerevisiae is a model polyprotein-encoding gene: the prohormone product is processed to release a variable number of copies of the mating pheromone α-factor. MFα1 is the source of nearly all of the α-factor produced by a yeast cell, but is not necessary for mating as the small amount of pheromone produced from its paralog MFα2 is sufficient for conjugation. However, when yeast cells compete for mates, cells producing the highest level of α-factor are most likely to be successful. Thus, synthesis of the MFα1 gene product is directly related to yeast sexual fitness. We show that the number of mature pheromone repeats encoded by MFα1 varies considerably between even closely related strains, and that repeat number is positively correlated with both the amount of pheromone secreted by a cell and its competitive mating success. However, increasing repeat number beyond the maximum observed in nature fails to further improve pheromone production or mating success. The basis of these diminishing returns is not associated with MFα1 transcript levels or with bottlenecks in protein processing or secretion. Instead, we propose that transcripts with more repeats are translated less efficiently than those with fewer repeats, a widespread phenomenon termed "length-dependent translation". Consistent with this hypothesis, we show that pheromone production and mating success are influenced both by MFα1 synonymous codon usage and by the putative regulator of length-dependent translation Asc1.

Survival, bet-hedging, and sex: What's a spore for?Primrose Boynton, MPI Plön

In fungal spores, recombination is often coupled to resistance to environmental stress. Both sex and resistance are possible adaptations to unpredictable environmental selection, but it is not obvious why they would be coupled. Why would a fungus not produce resistant asexual spores or susceptible sexual spores, especially if resistance and sex are costly? We investigated interactions between spore resistance and sex in the life cycle of the model yeast Saccharomyces cerevisiae, which produces resistant haploid ascospores from diploid parent cells. Each S. cerevisiae genotype has its own heritable sporulation efficiency--sporulation efficiency is the percentage of genetically identical cells which form spores in response to starvation. Once a food source is reintroduced, non-sporulated cells have the opportunity to grow quickly, while sporulated cells must germinate and mate before reaching their optimal growth rates. Sporulation efficiency is therefore a bet-hedging trait, and theory predicts that it evolves as a function of the frequency of strong selective events. The theoretical prediction disregards the influence of sex, which may further influence sporulation efficiency in unpredictable environments. We explored the evolution of sporulation efficiency by selecting S. cerevisiae populations under unpredictable conditions. We expected sporulation efficiency to closely match the frequency of strong selection, but not the absolute number of selective treatments, if resistance and bet-hedging were important to life cycle completion. Sporulation efficiency did indeed evolve to match selective treatment frequency in many selective lines. However, some lines that had experienced high selection also evolved vegetative resistance and low sporulation efficiencies; sporulation efficiency became decoupled to selection frequency in these lines. The selective treatments most likely increased the frequency of sexual recombination until cells with resistant gene combinations appeared, and the resulting populations subsequently evolved low sporulation efficiencies. In our selective regime, sporulation was only advantageous until sexual recombination could produce a cell that needed neither resistant spores nor further recombination.

Who’s driving? Host-parasite evolution in the bryophilous genus LizoniaMarie Davey, University of Oslo

The genus Lizonia is an exclusively bryophilous lineage with a unique life history. The fungus is a parasite occurring specifically on the male reproductive structures of polytrichaceous mosses. A single fungal perithecium completely replaces each male antheridium, effectively castrating the plant and diverting the resources the plant has allocated to reproduction. The genus was historically thought to be a member of the Pseudoperisporiaceae, but recent phylogenetic studies have pointed towards an affinity to the Pleosporales. A three gene phylogeny was built, confirming Lizonia’s membership in the Didymellaceae (Pleosporales). The genus-level phylogeny did not fully reflect traditional morphology-based classifications, and was strongly structured by host specificity. Two new species are described accordingly, and the traditional definitions of the previous species are made more strict. Cophylogenetic analysis between the host family (Polytrichaceae) and Lizonia identifies some co-phylogentic events where host evolution may have driven diversification in the parasite. However, host-switch and duplication events were more frequent and more likely for the

majority of species, indicating that the primary force driving speciation in Lizonia is the expansion and adaptation to new polytrichaceous hosts, a scenario that is consistent with a relatively modern shift to bryophilous hosts, rather than an evolutionarily long association. 

Host-parasite coevolution in a domesticated worldChaitanya Gokhale, MPI Plön

Host-parasite interactions are often studied in great detail both theoretically and experimentally as standard example of co-evolutionary dynamics. When domesticating animals or plants, via directed breeding or intensive agricultural techniques, the genetic makeup of the organisms is being modified. Especially focusing on plants and their pathogens, this can often neglect a major component capable of modifying this co-evolutionary process, agriculture. This certainly has an impact on the pathogens which have coevolved with these hosts of interest. Through theoretical studies we analyse how the co-evolutionary process between plants and their pathogens is affected by agriculture and how, unwittingly, we might be domesticating not just the plants but their pathogens as well.

Evolutionary genomics and population genetic analyses of the Zymoseptoria species complexChristoph Eschenbrenner, Ines Braker, Jonathan Grandaubert, Eva H. Stukenbrock, Christian-Albrechts University

One major biological thread for wheat production worldwide is the hemibiotrophic fungal wheat pathogen Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB). This highly specialized wheat pathogen causes high economical damages worldwide. With three closely related wild grass pathogens Z. ardabiliae, Z. pseudotritici and the recently identified Z. brevis, Z. tritici forms the Zymoseptoria species complex. Their recent divergence on different hosts, make this species complex an excellent model system for the analysis of pathogen speciation, species evolution and host specialization. We here aim to link genome wide population genetics parameters (Fixation index, FST and Tajima’s D) with patterns of positive selection (gene-wise ratios of non- synonymous and synonymous substitutions, dN/dS) assessed by maximum likelihood analyses in Z. tritici, Z. ardabiliae and Z. brevis . This procedure will enable us to identify patterns of selection across genomes within each species. Comparisons of positively selected genes in Z. brevis, Z. ardabiliae and Z. tritici will provide insight into different genetic components important for host specialization in these species. Genome wide analyses of Tajima’s D will provide information about the impact of different demographic events on the evolution of these pathogen species.

Genome Evolution of the Fungal Grass Pathogen Zymoseptoria pseudotriticiEzgi Özkurt, MPI Plön

Hybridization is proposed to be a major force in the speciation of fungal plant pathogens. The ascomycete grass pathogen Zymoseptoria pseudotritici emerged

recently from an interspecifc cross between yet unknown parental species. In a previous study, the genomes of ve individuals of Z. pseudotritici were sequenced and revealed a peculiar nucleotide diversity pattern: The genome consists of segments of high nucleotide diversity but comprising only two diverged haplotypes. The other segments comprising more than 40% of the genome are completely depleted of variation. This particular genome structure results from a cross between only two parental individuals that gave rise to a hybrid swarm that has recombined but never back-crossed to the parental species. Z. pseudotritici provides a unique model system to study genomics of a young hybrid species. Hence we set out to investigate patterns of selection and distribution of derived mutations by sequencing additional 22 individuals. Re-analyzing the new sequence alignment, we could confirm the diversity patterns of the genome as found among only five individuals. We assessed the site frequency spectrum to further investigate the distribution of variation in our population sample. The distribution of the allele frequencies was found to be remarkably different from the pattern in close relative species Z. tritici reflecting the different evolutionary histories of the species. Moreover, we assessed genome-wide signatures of positive selection. Some of the genes identified to be evolving under positive selection encode secreted proteins, and are putative effector candidates involved in host-pathogen interactions. We are currently applying additional analyses to estimate age the hybridization and the amount of variation in the whole population.

Marine Fungi - identification, genomics and transcriptomicsFrank Kempken, Christian-Albrechts University

The number of species and distribution of marine fungi is largely unknown. Likewise their role in marine ecology is mostly ignored so far. Yet, from a few model studies it is clear that marine fungi provide a fresh resource for secondary metabolites, which differs from terrestrial fungi. My research aims to identify cultivatable marine fungi from marine sources, as this environment appears to contain many fungal species with presumably unique adaptions to deep-sea conditions. While we are awaiting a large sample set from the Mid-Atlantic ridge, we already did identify more than 60 fungal species from 16 seafloor samples from the Baltic Sea. We analyzed secondary metabolite genes of marine-derived fungi, including a marine sponge-derived fungal strain of Scopulariopsis brevicaulis (Kumar et al., 2015) producing the anticancer drugs scopularids A and B (Lukassen et al., 2015). Two fungi from the North Sea mudflats, Calcarisporium sp. and Pestalotiopsis sp. contain 60 and 67 predicted secondary metabolite gene clusters respectively. This is the highest number of secondary metabolite gene clusters predicted so far (Kumar and Kempken, n.d.). Likewise a very large number of secondary metabolite gene clusters was identified in a Fusarium isolate from the Baltic Sea, that is currently under investigation as part of an ITN EU project “QUANT FUNG” (Phule and Kempken, unpublished).