Yvonne Poeschl

Caraway (Carum carvi L.) is a major essential oil crop with biennial and annual flowering types. As basic research resource, we developed a draft genome assembly using long-read ONT sequencing and provide a structural and functional gene annotation for an annual caraway inbred line. To elucidate the genetic control of flowering, a genotyping-by-sequencing (GBS) was conducted for an F₂ population (N = 187) generating 731 strictly filtered SNPs. A linkage map was constructed spanning 663 cM across 10 linkage groups with in total 634 (full map) or 259 (thinned map) SNPs. Contrary to its dominance in F₁, annual flowering occurred in only 36% of F₂ plants under late sowing conditions. Furthermore, the annual F₂ plants exhibited delayed flowering compared to the annual parent. QTL analysis identified five significant QTLs for (adjusted) flowering time (LG02, LG03, LG05, LG08 and LG10) explaining 6.1% to 10.5% (in total 42.7%) of phenotypic variance. The results support a polygenic predominately additive model for flowering induction in caraway. In addition, two QTLs for flower color (LG01, LG10) were detected explaining 10.9% and 26.0% of phenotypic variance, respectively. This study provides a comprehensive genomic resource for caraway, bridging the gap between traditional breeding and molecular improvement.

Microbial interactions in agricultural ecosystems are chemically dynamic, with significant implications for ecological balance and crop protection. As synthetic fungicides face increasing regulatory and resistance challenges, applying microbial biological control agents (MBCAs) presents a potential alternative crop-protection strategy. However, the chemical and toxicological consequences of such applications remain poorly understood. Using the model ascomycete Aspergillus nidulans , the response to confrontations with twelve microbial partners, including bacterial and fungal MBCAs, plant pathogens, and phylloplane isolates was studied. Dual-culture assays revealed distinct interaction patterns, and transcriptome profiling showed confrontation-specific activation of secondary metabolite biosynthetic gene clusters (SMBGCs), with up to 50 SMBGCs differentially expressed in A. nidulans . Complementary untargeted LC-MS/MS identified hundreds of unique secondary metabolites (SMs), including compounds structurally resembling synthetic fungicides, including azoles and piperidines. Notably, cytotoxicity assays using human HEK-293 and HCT-116 cell lines revealed that SM mixtures from confrontations of A. nidulans with Bacillus subtilis or Trichothecium roseum exhibited significant toxicity, with IC₅₀ values as low as 52 µg/mL. These findings demonstrate that microbial confrontations can trigger the production of diverse and specific sets of SMs, including compounds representing potential human health risks. This study underscores the need for confrontation-informed toxicological assessments in MBCA regulation and highlights the importance of developing safer biocontrol strategies in agriculture. IMPORTANCE: This study shows fundamental changes at the transcriptome and metabolome level in the ubiquitous fungus Aspergillus nidulans confronting various microorganisms, including microbial biological control agents. Strong modulations of transcript abundances of genes belonging to secondary metabolism gene clusters correlated with the formation of a vast array of novel secondary metabolites. Compounds formed in some confrontations were toxic to human cells, questioning the consumer safety of applying microbial biological control agents.

Premise: Plants produce a tremendous variety of secondary compounds that are crucial to interspecific and intraspecific interactions and for adaptation to environmental changes. This chemical diversity has been attributed to multiple factors, including interactions with herbivores or pollinators, tissue‐specific needs, and evolutionary constraints. The interplay between a vast array of factors driving plant chemodiversity remains unclear, mainly because most studies have focused on a single organ—mostly leaves—or, when comparing different organs, have been limited to single taxa. Thus, the relationship between functional and phylogenetic factors remains unresolved. We use a model system of Ficus from Madagascar to examine the extent to which phytochemical diversity is shaped by tissue‐specific function and the degree to which phylogenetic relatedness explains variation in fruit and leaf chemodiversity.Methods: We applied an untargeted metabolomics approach to unripe fruits (the syconium, a hollow structure containing numerous small flowers) and leaves from eight species of wild figs (Ficus spp.) sampled in a tropical rainforest in Madagascar. We characterized their chemical profiles using ultra‐performance liquid chromatography–mass spectrometry and reconstructed their phylogeny using six genetic markers to understand the patterns of chemodiversity.Results: Fruit and leaf metabolomes were more similar to the same organ in other species than to the other organs within the same species. There was a significant but moderate phylogenetic correlation in fruit and leaf chemodiversity.Conclusions: Although phylogenetic relatedness influences plant chemodiversity in Malagasy figs, functional convergence of tissue‐specific metabolites may be a major evolutionary driver.

Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant‐colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans . Transcriptome studies uncovered strong de‐regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69% and 86% of these clusters de‐regulated at confrontation sites with B. amyloliquefaciens or A. nidulans , respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100% and 74% of the SMBGCs were transcriptionally de‐regulated, respectively. Correspondingly, non‐targeted high‐resolution LC–MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus–bacterium and fungus–fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.

Insect herbivory is a key process in ecosystem functioning. While theory predicts that plant diversity modulates herbivory, the mechanistic links remain unclear. We postulated that the plant metabolome mechanistically links plant diversity and herbivory. In late summer and in spring, we assessed individual plant above‐ground herbivory rates and metabolomes of seven plant species in experimental plant communities varying in plant species diversity and resource acquisition strategies. In the same communities, we also measured plant individual biomass as well as soil microbial and nematode community composition. Herbivory rates decreased with increasing plant species richness. Path modelling revealed that plant species richness and community resource acquisition strategy correlated with soil community composition. In particular, changes in nematode community composition were related to plant metabolome composition and thereby herbivory rates. Synthesis. These results suggest that soil community composition plays an important role in reducing herbivory rates with increasing plant diversity by changing plant metabolomes.

Belowground herbivores are overseen and underestimated, even though they can cause significant economic losses in agriculture. The cabbage root fly Delia radicum (Anthomyiidae) is a common pest in Brassica species, including agriculturally important crops, such as oilseed rape. The damage is caused by the larvae, which feed specifically on the taproots of Brassica plants until they pupate. The adults are aboveground‐living generalists feeding on pollen and nectar. Female flies are attracted by chemical cues in Brassica plants for oviposition. An assembled and annotated genome can elucidate which genetic mechanisms underlie the adaptation of D. radicum to its host plants and their specific chemical defences, in particular isothiocyanates. Therefore, we assembled, annotated and analysed the D. radicum genome using a combination of different next‐generation sequencing and bioinformatic approaches. We assembled a chromosome‐level D. radicum genome using PacBio and Hi‐C Illumina sequence data. Combining Canu and 3D‐DNA genome assembler, we constructed a 1.3 Gbp genome with an N50 of 242 Mbp and 6 pseudo‐chromosomes. To annotate the assembled D. radicum genome, we combined homology‐, transcriptome‐ and ab initio‐prediction approaches. In total, we annotated 13,618 genes that were predicted by at least two approaches. We analysed egg, larval, pupal and adult transcriptomes in relation to life‐stage specific molecular functions. This high‐quality annotated genome of D. radicum is a first step to understanding the genetic mechanisms underlying host plant adaptation. As such, it will be an important resource to find novel and sustainable approaches to reduce crop losses to these pests.

Plants produce thousands of compounds, collectively called the metabolome, which mediate interactions with other organisms. The metabolome of an individual plant may change according to the number and nature of these interactions. We tested the hypothesis that tree diversity level affects the metabolome of four subtropical tree species in a biodiversity–ecosystem functioning experiment, BEF‐China. We postulated that the chemical diversity of leaves, roots and root exudates increases with tree diversity. We expected that the strength of this diversity effect differs among leaf, root and root exudates samples. Considering their role in plant competition, we expected to find the strongest effects in root exudates. Roots, root exudates and leaves of four tree species (Cinnamomum camphora, Cyclobalanopsis glauca, Daphniphyllum oldhamii and Schima superba) were sampled from selected plots in BEF‐China. The exudate metabolomes were normalized over their non‐purgeable organic carbon level. Multivariate analyses were applied to identify the effect of both neighbouring (local) trees and plot diversity on tree metabolomes. The species‐ and sample‐specific metabolites were assigned to major compound classes using the ClassyFire tool, whereas potential metabolites related to diversity effects were annotated manually. Individual tree species showed distinct leaf, root and root exudate metabolomes. The main compound class in leaves was the flavonoids, whereas carboxylic acids, prenol lipids and specific alkaloids were most prominent in root exudates and roots. Overall, plot diversity had a stronger effect on metabolome profiles than the local diversity. Leaf metabolomes responded more often to tree diversity level than exudates, whereas root metabolomes varied the least. We found no uniform or general pattern of alterations in metabolite richness or diversity in response to variation in tree diversity. The response differed among species and tissues. Synthesis. Classification of metabolites supported initial ecological interpretation of differences among species and organs. Particularly, the metabolomes of leaves and root exudates respond to differences in tree diversity. These responses were neither linear nor uniform and individual metabolites showed different dynamics. More controlled interaction experiments are needed to dissect the causes and consequences of the observed shifts in plant metabolomes.

Belowground herbivores are overseen and underestimated, even though they can cause significant economic losses in agriculture. The cabbage root fly Delia radicum (Anthomyiidae) is a common pest in Brassica species, including agriculturally important crops, such as oil seed rape. The damage is caused by the larvae, which feed specifically on the taproots of Brassica plants until they pupate. The adults are aboveground-living generalists feeding on pollen and nectar. Female flies are attracted by chemical cues in Brassica plants for oviposition. An assembled and annotated genome can elucidate which genetic mechanisms underlie the adaptation of D. radicum to its host plants and their specific chemical defenses, in particular isothiocyanates. Therefore, we assembled, annotated and analyzed the D. radicum genome using a combination of different Next Generation Sequencing and bioinformatic approaches. We assembled a chromosome-level D. radicum genome using PacBio and Hi-C Illumina sequence data. Combining Canu and 3D-DNA genome assembler, we constructed a 1.3 Gbp genome with an N50 of 242 Mbp and 6 pseudo-chromosomes. To annotate the assembled D. radicum genome, we combined homology-, transcriptome- and ab initio -prediction approaches. In total, we annotated 13,618 genes that were predicted by at least two approaches. We analyzed egg, larval, pupal and adult transcriptomes in relation to life-stage specific molecular functions. This high-quality annotated genome of D. radicum is a first step to understanding the genetic mechanisms underlying host plant adaptation. As such, it will be an important resource to find novel and sustainable approaches to reduce crop losses to these pests.

Spatiotemporal control of cell division is essential for the growth and development of multicellular organisms. In plant cells, proper cell plate insertion during cytokinesis relies on the premitotic establishment of the division plane at the cell cortex. Two plant-specific cytoskeleton arrays, the preprophase band (PPB) and the phragmoplast, play important roles in division-plane orientation and cell plate formation, respectively¹. Microtubule organization and dynamics and their communication with membranes at the cortex and cell plate are coordinated by multiple, mostly distinct microtubule-associated proteins². How division-plane selection and establishment are linked, however, is still unknown. Here, we report members of the Arabidopsis IQ67 DOMAIN (IQD) family³ as microtubule-targeted proteins that localize to the PPB and phragmoplast and additionally reside at the cell plate and a polarized cortical region including the cortical division zone (CDZ). IQDs physically interact with PHRAGMOPLAST ORIENTING KINESIN (POK) proteins^4,5 and PLECKSTRIN HOMOLOGY GTPase ACTIVATING (PHGAP) proteins⁶, which are core components of the CDZ¹. The loss of IQD function impairs PPB formation and affects CDZ recruitment of POKs and PHGAPs, resulting in division-plane positioning defects. We propose that IQDs act as cellular scaffolds that facilitate PPB formation and CDZ set-up during symmetric cell division.