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URPP Evolution in Action: From Genomes to Ecosystems

Evolution of Pathogens, Parasites, and Pathosystems

The co-evolutionary race of pathogens and their hosts provides a unique opportunity to study mechanisms of adaptation and diversification in evolution. Both pathogen evolution and host adaptation have been major topics in research and teaching in the first two phases of the URPP Evolution in Action and will remain an important research field in the third phase. Many co-evolutionary events in host–pathogen interactions occur within very short time frames, i.e. within a few years or at least a few hundred years, and therefore represent excellent opportunities to study “evolution in action”. Furthermore, host-pathogen systems are studied in the lab and in the field, from the molecular and cellular level to ecosystems and landscapes. Thus, they are ideally suited as a focus in Phase III of the URPP Evolution in Action with a large number of topics that can be addressed in specific research projects. Advances in sequencing and genome analysis have made comparative genome analysis an increasingly powerful tool for understanding pathogen (viral and bacterial) evolution for human and animal diseases, but also in the natural and agricultural environments (mostly fungal pathogens). The environments where pathogens cause damage differ greatly in the type of selection pressure and adaptation events which result in a successful pathogen. Thus, studies in each of these environments are revealing fundamental insights on a diversity of adaptation strategies, which can result in diversification and ultimately the emergence of new species. For Research Core Area 1, the following five projects addressing various aspects of the topic were selected:

Mining Herbaria to Explore Phylogeography and Coevolution in Plant Pathosystems: the Case of the Irish Potato Famine Pathogen Phytophthora infestans and its Solanaceous Hosts

Simon Aeschbacher (EBES), Verena Schünemann (IEM), Jurriaan de Vos (University of Basel)

Host–pathogen interactions are principle drivers of evolution. While host–pathogen coevolution often leads to stable coexistence in natural systems, many domesticated species lack the adaptive potential to keep up with their pathogens in the evolutionary arms race. Aggressive pathogen strains escaping their host’s defense mechanisms have devastating potential when causing disease in livestock and crops. Strategies against aggressive pathogen strains requires a detailed understanding of the molecular and evolutionary host–pathogen interactions. Such understanding requires an interdisciplinary effort. Mining herbaria for plant pathogen ancient DNA (aDNA) is a promising approach. Unleashing the potential of herbaria for the study of plant pathosystems requires a cost-effective, minimally destructive, and aDNA-specific workflow, and statistical approaches that make explicit use of time-referenced samples.

Here, we use the Irish potato famine pathogen Phytophthora infestans and its hosts as a model to develop a molecular approach for efficiently screening herbarium tissue for the presence of focal pathogen aDNA. Combining historical and modern DNA isolated from tomato and potato specimens, we analyze the past and present genetic diversity in P. infestans, establish a phylogeny, and infer evolutionary processes using time-referenced population genomic approaches. In parallel, we scan the genomes of a subset of the host specimens for signals of demography and natural selection. Ultimately, we aim at jointly analyzing the pathogen and host data to identify patterns of concerted evolution, both at a genomic scale and at known pathogen effectors and plant resistance genes. Reaching these objectives requires integration of an aDNA clean-lab and next-generation sequencing technology, population genomic theory, and statistical analyses of genome-scale data.

The project will deliver a proof-of-concept for obtaining whole-genome host and pathogen DNA from herbaria at a scale that facilitates the study of (co-)evolution in a range of plant pathosystems, including an array of rust fungi and oomycetes causing severe losses in crops and vegetables. The project will result in a set of inferential approaches that exploit the spatiotemporal information associated with historical records and make efficient use of aDNA.

PhD-Student: Donikë Sejdiu

Molecular Identification of Plant Immunity Genes Involved in Non-Host Resistance of Triticale to the Wheat Powdery Mildew Pathogen

Beat Keller (IPMB), Kentaro Shimizu (EBES), Thomas Wicker (IPMB)

Adaptation of pathogens to novel hosts is frequently occurring over short time periods and represents an example of "evolution in action". Such adaptation has been observed in human, animal, and plant pathogens. Recent adaptation of pathogens to crop plants has also been observed in agricultural environments. For example, wheat blast emerged recently because of the unfortunate use of some novel wheat cultivars lacking specific immune receptors. Furthermore, we have shown in Phase I of the URPP Evolution in Action that the newly emerged powdery mildew pathogen on the man-made crop triticale was formed by a rare hybridization of two mildew forms.

This project is a continuation and completion of work successfully performed by two graduate students (Fabrizio Menardo, Marion Müller) in the first two phases of the URPP Evolution in Action. Within Phase II, we completed the work on the identification of two candidate effectors in mildew that are involved in host adaptation. These effectors were functionally validated in 2020. Thus, on the pathogen side, the first molecular determinants of host specificity are identified. In this follow-up proposal here, we aim at the identification of the corresponding immune receptors in triticale that define the specificity of the interaction in the host plant. The combined work of Phases II and III will result for the first time in the identification of the molecular determinants of non-host resistance in both the host plant and the pathogen.

To achieve this, we first want to define the chromosomal location in the triticale genome of two genes (possibly encoding immune receptors) involved in non-host resistance to wheat powdery mildew based on the two avirulence genes identified in the pathogen in Phase II. Genetic mapping will be performed in a cross of two triticale varieties differing in the presence of the two non-host resistance genes. Based on chromosomal information, we will then identify the target genes by mutagenesis and the application of genomic tools and approaches such as MutChromSeq that are well established in our groups. The identified candidate genes will finally be validated using functional approaches.

Visiting Collaborator: Dr. Harsh Chauhan

Former Postdoc: Dr. Marion Müller

Does Selection for Disease Resistance Vary along an Elevation Gradient?

Anna-Liisa Laine (EBES), Andreas Wagner (EBES)

Understanding the drivers that generate variation in life-history traits is one of the core challenges in Evolutionary Biology. Natural populations exhibit considerable diversity in disease resistance, although fitness of most organisms may depend on their ability to resist pathogens. Theory predicts resistance to evolve under pathogen-imposed selection, yet evidence for pathogen-mediated selection to generate the observed diversity in resistance has remained scarce. Biodiversity and ecosystem productivity increase dramatically toward low latitudes and elevations, generating corresponding increases in the intensity of species interactions. While the evolutionary consequences of such variation in the intensity of species interactions are largely unknown, we would expect to see a gradual decrease in the strength of pathogen-mediated selection for resistance with increasing elevation. 

To test this hypothesis, we will study resistance variation in Plantago lanceolata across an elevation gradient (600-1600 m) in the Calanda mountain of Switzerland through a combination of field transplantation and laboratory inoculation experiments, and an analysis of variation at resistance-relevant genes. We will first carry out a laboratory inoculation study and a field transplant experiment to determine whether resistance variation against the fungal pathogen Podosphaera plantaginis varies according to elevation, and whether this variation is explained by local selection. To understand how resistance varies against a broad range of pathogens, we will also quantify genetic diversity and signatures of selection in the recently characterized NLR protein-coding genes of P. lanceolata across the elevation gradient.

This project will be the first to identify the role of altitude in generating spatial variation of disease resistance in plants. It will improve our ability to understand and predict how diversity - both among and within species - is spatially structured. More generally, it will also improve our understanding of host-pathogen interactions, community organization, and life-history evolution.

PhD-Student: Michael Rechsteiner​​​​​​​

Investigating the Evolution of Mycobacterial Infections through the Combination of Biomolecular Methods

Verena Schuenemann (IEM), Matthew Collins (University of Copenhagen), Frank Rühli (IEM)

Tuberculosis (TB) and leprosy are two major diseases that present as a global burden today with an estimated 1.4 million new cases of TB and 200,000 for leprosy each year. Although each disease has plagued human populations throughout much of our history, little is known about their origins and initial spread into human populations. In order to understand the evolutionary pathways of these pathogens, researchers can identify archaeological individuals with TB or leprosy, and sequencing the ancient pathogen genomes.

Here, we will apply a strategy of combined genomic (NGS) and proteomic (LC-MS/MS) analyses to investigate the evolution of pathogenic mycobacteria, M. tuberculosis and M. leprae, in order to increase our understanding of the pathways each followed. As mycobacterial infections have, through natural selection and genetic drift, evolved to be extremely successful in infecting human hosts, understanding the avenues through which these pathogens evolved will better assist clinical researchers in discovering new and effective ways to combat antibiotic resistance. In addition to the identification of new genomes through NGS, we also aim to identify proteins associated with human immune response to confirm active infection in historic and archaeological individuals. 

The study will begin by testing modern tuberculosis (TB) and leprosy bacteria to determine the gene and proteins commonly recovered. We will then assess formalin-fixed tissues from historic individuals with known infections by either disease at their time of death to find which biomarkers persist into the recent past. Finally, we will utilize the same methods on bone samples from archaeological individuals with paleopathological lesions indicative of each disease. Our findings should greatly increase the number of known ancient TB and leprosy genomes, and the creation of combined genomic and proteomic datasets will allow us to understand the sensitivity of each method, and whether the use of both in tandem can offer new insights into infection and human immune responses. The successful identification of peptide biomarkers specific to TB or leprosy may offer a quick and inexpensive way to identify historic and ancient samples best suited for ancient pathogen DNA analysis through peptide mass fingerprinting.

Postdoc: Dr. Shevan Wilkin

Rapid Evolution of a Pathogen Recapitulates the Hybridization of Host Polyploid Wheat

Kentaro Shimizu (EBES), Beat Keller (IPMB), Shuhei Nasuda (Kyoto University), Thomas Wicker (IPMB)

The evolution of wheat and its powdery mildew pathogen has been one of the best studied systems of the molecular basis of host–pathogen evolution. In Phase II of the URPP Evolution in Action, a genome-wide polymorphism study of the fungal pathogen causing powdery mildew, Blumeria graminis, was conducted. Admixture analysis showed that B. graminis in Japan had a hybrid origin combining Western and Eastern strains. This is in parallel with the origin of modern Japanese wheat cultivars derived from the crosses of Western and Eastern strains during the past ~50 years. Thus, the data suggest a rapid coevolution of the pathogen and its host, in which the hybridization of the host by selective breeding was rapidly followed by hybridization of the pathogen. To test this hypothesis of the evolution of host–pathogen by hybridization, a major obstacle is the complex genome of the host wheat because of its polyploidy (allohexaploid with three homeologs) and the huge genome size (about 17 Gb) with a massive number of repetitive elements. However, advances in sequencing technology and bioinformatic algorithms aimed at polyploid species have allowed high-quality genome assembly and polymorphism analysis. The PIs have completed de novo sequencing of the genomes of European and Asian wheat as part of the wheat 10+ genome consortium (chromosome-scale assembly, N50 >20 Mb). Furthermore, the high-coverage resequencing of 25 Asian accessions that encompass both traditional Asian landraces and cultivars derived from the crosses of those Asian landraces and Western cultivars will be available. We hypothesize that hybridization of the European and Asian wheat changed the specificity of host–pathogen recognition. First, we will quantify the mildew susceptibility of the 25 core wheat cultivars. Second, chromosomal regions of European origin among Asian accessions will be identified from single nucleotide polymorphisms (SNP) data and the distribution of transposable elements using high-coverage resequencing data. Third, the susceptibility loci will be mapped using nested association mapping lines, which combine the advantage of QTL and association mapping. We will test whether both genomic regions - of European and Asian origins - contributed to interactions in the hybrid Blumeria. 

PhD-Student: Naoto-Benjamin Hamaya​​​​​​​