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9. Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis.

Author

Vidal‐Villarejo, Mireia, Dößelmann, Bianca, Kogler, Benedikt, Hammerschmidt, Michael, Oppliger, Barbara, Oppliger, Hans, and Schmid, Karl

Subjects
PHYTOPATHOGENIC microorganisms, BIOLOGICAL pest control agents, AGRICULTURE, PSEUDOPOTENTIAL method, DNA sequencing
Abstract

The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco‐evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016–2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen–microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Schmitz, Robert J, Urich, Mark A, Castanon, Rosa, Nery, Joseph R, Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, Wang, Congmao, Bemm, Felix, Becker, Claude, O’Neil, Ryan, O’Malley, Ronan C, Quarless, Danjuma X, Consortium, The 1001 Genomes, Alonso-Blanco, Carlos, Andrade, Jorge, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R, Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G, Hancock, Angela, Henz, Stefan R, Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A, Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P, Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F Xavier, Platzer, Alexander, Rabanal, Fernando A, Rodriguez, Alex, Rowan, Beth A, Salomé, Patrice A, Schmid, Karl, Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M, Todd, Donald, Volchenboum, Samuel L, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, and Schork, Nicholas J

Subjects
Human Genome, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Arabidopsis, DNA Methylation, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Plant, Genome, Plant, Transcriptome, Genomes Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Published
2016

26. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., and Schork, Nicholas J.

Published
2016
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27. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Published
2016
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36. Population genomic evidence for a repeated introduction and rapid expansion of the fungal maize pathogen Setospheria turcica in Europe

Author

Vidal-Villarejo, Mireia, Freund, Fabian, Hanekamp, Hendrik, von Tiedemann, Andreas, and Schmid, Karl

Abstract

Northern corn leaf blight (NCLB) is a devastating fungal disease of maize and caused by the fungal pathogen Setosphaeria turcica. We show by sequencing of S. turcica isolates and evolutionary modeling that over the last 30 years different clonal, asexually reproducing lineages of the pathogen emerged and spread throughout Central and Western Europe. This likely resulted from an expansion of the cultivation area and modern agricultural practices, we do not find evidence that strong selection was a major driver of the development within clonal lineages. New pathogen races, which are virulent to single resistance genes used in maize breeding, seem to have evolved independently within different clonal lineages by spontaneous mutations.

Published
2023
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38. Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana

Author

Latzel, Vít, Fischer, Markus, Groot, Maartje, Gutzat, Ruben, Lampei, Christian, Ouborg, Joop, Parepa, Madalin, Schmid, Karl, Vergeer, Philippine, Zhang, Yuanye, Bossdorf, Oliver, Latzel, Vít, Fischer, Markus, Groot, Maartje, Gutzat, Ruben, Lampei, Christian, Ouborg, Joop, Parepa, Madalin, Schmid, Karl, Vergeer, Philippine, Zhang, Yuanye, and Bossdorf, Oliver

Abstract

The phenotypes of plants can be influenced by the environmental conditions experienced by their parents. However, there is still much uncertainty about how common and how predictable such parental environmental effects really are. We carried out a comprehensive experimental test for parental effects, subjecting plants of multiple Arabidopsis thaliana genotypes to 24 different biotic or abiotic stresses, or combinations thereof, and comparing their offspring phenotypes in a common environment. The majority of environmental stresses caused significant parental effects, with −35% to +38% changes in offspring fitness. The expression of parental effects was strongly genotype-dependent, and multiple environmental stresses often acted nonadditively when combined. The direction and magnitude of parental effects were unrelated to the direct effects on the parents: Some environmental stresses did not affect the parents but caused substantial effects on offspring, while for others, the situation was reversed. Our study demonstrates that parental environmental effects are common and often strong in A. thaliana, but they are genotype-dependent, act nonadditively, and are difficult to predict. We should thus be cautious with generalizing from simple studies with single plant genotypes and/or only few individual environmental stresses. A thorough and general understanding of parental effects requires large multifactorial experiments.

Published
2023

39. Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Author

Kersten, Sonja, primary, Chang, Jiyang, additional, Huber, Christian D., additional, Voichek, Yoav, additional, Lanz, Christa, additional, Hagmaier, Timo, additional, Lang, Patricia, additional, Lutz, Ulrich, additional, Hirschberg, Insa, additional, Lerchl, Jens, additional, Porri, Aimone, additional, Van de Peer, Yves, additional, Schmid, Karl, additional, Weigel, Detlef, additional, and Rabanal, Fernando A., additional

Published
2023
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45. Population genomic analysis of the rapid expansion of the fungal pathogen Setosphaeria turcica in Europe

Author

Vidal-Villarejo, Mireia, Freund, Fabian, Schmid, Karl, Hanekamp, Hendrik, and Von Tiedemann, Andreas

Subjects
Demographic history, DDC 570 / Life sciences, ddc:580, Koaleszenztheorie, DDC 580 / Botanical sciences, ddc:570, Setosphaeria turcica, Transgenic plants, Coalescent theory, Population structure, Genetic diversity
Abstract

The maize fungal pathogen Setosphaeria turcica has been expanding into Central Europe since the 1980s. We analyse its genetic diversity sampled across Europe and compare it with genetic diversity outside of Europe. Using clustering, phylogenetic and coalescent-based approaches, we find evidence for several clonal lineages across Europe that are rapidly expanding and have only recently emerged. The genetic diversity within the clonal lineages does not seem to be shaped mainly by pervasive selection, but can be explained by a growing population, potentially due to the massive increase in maize production in Central Europe., publishedVersion

Published
2022

48. Deep haplotype analyses of target‐site resistance locus ACCase in blackgrass enabled by pool‐based amplicon sequencing.

Author

Kersten, Sonja, Rabanal, Fernando A., Herrmann, Johannes, Hess, Martin, Kronenberg, Zev N., Schmid, Karl, and Weigel, Detlef

Subjects
HAPLOTYPES, HERBICIDE application, WEED control, HERBICIDE resistance, PHENOTYPES, HERBICIDES, WEEDS
Abstract

Summary: Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in only a few generations. Target‐site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio's long‐read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons are costly and time‐consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool‐based approaches overcome these limitations and provide reliable allele frequencies, although at the expense of not preserving haplotype information. In this proof‐of‐concept study, we sequenced with PacBio High Fidelity (HiFi) reads long‐range amplicons (13.2 kb), encompassing the entire ACCase gene in pools of over 100 individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools in plants and other organisms. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analysed new pools from a Germany‐wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward‐in‐time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, highlighting the importance of accurate measurement of TSR haplotype prevalence for weed management. [ABSTRACT FROM AUTHOR]

Published
2023
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