The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of .50 species known as the Fusarium solani species complex . Members of this complex have diverse biological properties including the ability to cause disease on .100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion

The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

Evolution and genome architecture in fungal plant pathogens

The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum) Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z tritici on wheat leaves Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z tritici, which may instead be utilizing lipid and fatty acid stores for growth However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence The pathogenic lifestyle of Z tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection

Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition.

Zymoseptoria tritici is the causal agent of Septoria tritici blotch, a major pathogen of wheat globally and the most damaging pathogen of wheat in Europe. A gene-for-gene (GFG) interaction between Z. tritici and wheat cultivars carrying the Stb6 resistance gene has been postulated for many years, but the genes have not been identified. We identified AvrStb6 by combining quantitative trait locus mapping in a cross between two Swiss strains with a genome-wide association study using a natural population of c. 100 strains from France. We functionally validated AvrStb6 using ectopic transformations. AvrStb6 encodes a small, cysteine-rich, secreted protein that produces an avirulence phenotype on wheat cultivars carrying the Stb6 resistance gene. We found 16 nonsynonymous single nucleotide polymorphisms among the tested strains, indicating that AvrStb6 is evolving very rapidly. AvrStb6 is located in a highly polymorphic subtelomeric region and is surrounded by transposable elements, which may facilitate its rapid evolution to overcome Stb6 resistance. AvrStb6 is the first avirulence gene to be functionally validated in Z. tritici, contributing to our understanding of avirulence in apoplastic pathogens and the mechanisms underlying GFG interactions between Z. tritici and wheat.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.14434

A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene.

Two recent innovations, the emergence of formal cognitive models and the addition of cognitive neuroscience data to the traditional behavioral data, have resulted in the birth of a new, interdisciplinary field of study: model-based cognitive neuroscience. Despite the increasing scientific interest in model-based cognitive neuroscience, few active researchers and even fewer students have a good knowledge of the two constituent disciplines. The main goal of this edited collection is to promote the integration of cognitive modeling and cognitive neuroscience. Experts in the field will provide tutorial-style chapters that explain particular techniques and highlight their usefulness through concrete examples and numerous case studies. The book will also include a thorough list of references pointing the reader towards additional literature and online resources.

/pdf/an-introduction-to-model-based-cognitive-neuroscience-45ci3vj0pr.pdf

An introduction to model-based cognitive neuroscience

The speciation of pathogens can be driven by divergent host specialization. Specialization to a new host is possible via the acquisition of advantageous mutations fixed by positive selection. Comparative genome analyses of closely related species allows for the identification of such key substitutions via inference of genome-wide signatures of positive selection. We previously used a comparative genomics framework to identify genes that have evolved under positive selection during speciation of the prominent wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola). In this study, we conducted functional analyses of four genes exhibiting strong signatures of positive selection in Z. tritici. We deleted the four genes in Z. tritici and confirm a virulence-related role of three of the four genes ΔZt80707, ΔZt89160 and ΔZt103264. The two mutants ΔZt80707 and ΔZt103264 show a significant reduction in virulence during infection of wheat; the ΔZt89160 mutant causes a hypervirulent phenotype in wheat. Mutant phenotypes of ΔZt80707, ΔZt89160 and ΔZt103264 can be restored by insertion of the wild-type genes. However, the insertion of the Zt80707 and Zt89160 orthologs from Z. pseudotritici and Z. ardabiliae do not restore wild-type levels of virulence, suggesting that positively selected substitutions in Z. tritici may relate to divergent host specialization. Interestingly, the gene Zt80707 encodes also a secretion signal that targets the protein for cell secretion. This secretion signal is however only transcribed in Z. tritici, suggesting that Z. tritici-specific substitutions relate to a new function of the protein in the extracellular space of the wheat-Z. tritici interaction. Together, the results presented here highlight that Zt80707, Zt103264 and Zt89160 represent key genes involved in virulence and host-specific disease development of Z. tritici. Our findings illustrate that evolutionary predictions provide a powerful tool for the identification of novel traits crucial for host adaptation and pathogen evolution.

/pdf/rapidly-evolving-genes-are-key-players-in-host-xl4g70k227.pdf

Rapidly Evolving Genes Are Key Players in Host specialization and virulence of the fungal wheat pathogen Zymoseptoria tritici (Mycosphaerella graminicola)

Host specialization by pathogens requires a repertoire of virulence factors as well as fine-tuned regulation of gene expression. The fungal wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a powerful model system for the discovery of genetic elements that underlie virulence and host specialization. We transcriptionally profiled the early stages of Z. tritici infection of a compatible host (wheat) and a noncompatible host (Brachypodium distachyon). The results revealed infection regulatory programs common to both hosts and genes with striking wheat-specific expression, with many of the latter showing sequence signatures of positive selection along the Z. tritici lineage. Genes specifically regulated during infection of wheat populated two large clusters of coregulated genes that may represent candidate pathogenicity islands. On evolutionarily labile, repeat-rich accessory chromosomes (ACs), we identified hundreds of highly expressed genes with signatures of evolutionary constraint and putative biological function. Phylogenetic analyses suggested that gene duplication events on these ACs were rare and largely preceded the diversification of Zymoseptoria species. Together, our data highlight the likely relevance for fungal growth and virulence of hundreds of Z. tritici genes, deepening the annotation and functional inference of the genes of this model pathogen.

/pdf/expression-profiling-of-the-wheat-pathogen-zymoseptoria-2arv7ruckf.pdf

Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

A Predictive Approach to Nonparametric Inference for Adaptive Sequential Sampling of Psychophysical Experiments.

The question of how people change their opinions through social interactions has been on the agenda of social scientific research for many decades. Now that the Internet has led to an ever greater interconnectedness and new forms of exchange that seem to go hand in hand with increasing political polarization, it is once again gaining in relevance. Most recently, the field of opinion dynamics has been complemented by social feedback theory, which explains opinion polarization phenomena by means of a reinforcement learning mechanism. According to the assumptions, individuals not only evaluate the opinion alternatives available to them based on the social feedback received as a result of expressing an opinion within a certain social environment. Rather, they also internalize the expected and thus rewarded opinion to the point where it becomes their actual private opinion. In order to put the implications of social feedback theory to a test, we conducted a randomized controlled laboratory experiment. The study combined preceding and follow-up opinion measurements via online surveys with a laboratory treatment. Social feedback was found to have longer-term effects on private opinions, even when received in an anonymous and sanction free setting. Interestingly and contrary to our expectations, however, it was the mixture of supportive and rejective social feedback that resulted in the strongest influence. In addition, we observed a high degree of opinion volatility, highlighting the need for further research to help identify additional internal and external factors that might influence whether and how social feedback affects private opinions.

The effects of social feedback on private opinions. Empirical evidence from the laboratory

As an example for the third point, we refer to an ongoing research debate about the time course for early visual processing. For the detection and discrimination impairment of a stimulus by a closely followed second stimulus, two competing models exist (U-shaped vs. monotonically increasing, see [3]) that had been related to special types of experiments each. Recent experimental results, however, demonstrate severe violations of these experimental assumptions [4,5], but the question whether any of these two models is appropriate at all remains open. A suitable nonparametric inference might help to find better descriptions of the experimental data and finally to develop new models with only a few parameters.

/pdf/a-nonparametric-bayesian-approach-to-adaptive-sampling-of-4zt6jed39r.pdf

Stephan Poppe

Papers

Rapidly Evolving Genes Are Key Players in Host specialization and virulence of the fungal wheat pathogen Zymoseptoria tritici (Mycosphaerella graminicola)

Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

A Predictive Approach to Nonparametric Inference for Adaptive Sequential Sampling of Psychophysical Experiments.

The effects of social feedback on private opinions. Empirical evidence from the laboratory

A nonparametric Bayesian approach to adaptive sampling of psychometric functions