Biology subjects

Bouwmeester, K.

Publications and source records attributed to Bouwmeester, K..

5 recordsLinked to original sources

bioRxiv2026

Systematic mass-spectrometry-guided metabolic fingerprinting elucidates diversity of specialized metabolites across the Brassicaceae

O_LIPlants produce diverse bouquets of specialized metabolites (SMs), yet only a fraction of the vast phytochemical space has been explored to date. Comparative analysis of SM profiles can reveal hotspots of biochemical novelty, while systematic profiling across taxonomic levels does presently not cover large plant families. C_LIO_LITo study core and accessory SM profiles in the Brassicaceae plant family, we fingerprinted 14 species by Liquid-Chromatography Mass-Spectrometry (LCMS/MS). We develop standardized experimental and computational workflows integrating in silico annotation tools to study consensus compound class and substructure distributions of SMs. Furthermore, we investigate the congruence of chemotaxonomy and species phylogeny across an extended panel of 17 species. C_LIO_LIUnique metabolite profiles were outstanding in Camelina sativa, Capsella rubella, and B. vulgaris, with the largest unique terpenoid profile annotated in C. sativa, accounting for 33.5% and 55.6% in positive and negative ionization mode, respectively. Substructure motifs were found to overlap with compound class predictions, highlighted for triterpenoids in Camelinodae. Furthermore, dual-tissue chemotaxonomic clustering resembled relationships of Brassica subgenomes across tissues. C_LIO_LIWe anticipate that our systematic approach can serve as a blueprint for investigating biochemical diversity in other plant lineages and can boost the characterization of plant natural product pathways. C_LI

plant biology↗

bioRxiv2026

Metabolic fingerprinting of 17 Brassicaceae species across three tissues

Plants produce the most diverse blends of specialized metabolites on earth. Natural products derived from plants are valuable resources for drug development, food chemistry, and crop resistance breeding. Phenotypes of specialized metabolite profiles can be captured by untargeted mass-spectrometry across species phylogeny, tissues, and genotypes. Here, we collected metabolic fingerprints of 17 Brassicaceae species across three tissues (paired leaf and root; flower) using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in positive and negative ionization mode. Corresponding metadata has been refined for reuse according to ReDU guidelines, and for integration with public genomic and transcriptomic data. Standardization of in vitro growth conditions, and data processing workflows enables integration of acquired raw and processed data across platforms for single- and multi-omics analysis. Further, the inclusion of tissue-specific metabolic profiles across ploidy levels, as well as across crop species and wild relatives, makes this dataset a valuable resource for natural product discovery.

plant biology↗

bioRxiv2022

The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae

Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibilities (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non-host species. This phenomenon of resistance in L. saligna is called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant-pathogen interaction triggered by pathogen-recognition receptors, including nucleotide-binding leucin-rich repeats (NLRs) and receptor-like kinases (RLKs). We report a chromosome-level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis of Bremia infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidate(s) for determinants for the NHR phenotype of L. saligna.

genomics↗

bioRxiv2020

Variation in insect herbivore communities on individual plants reveal phylogenetic signal in uncertainty of attack in Brassicaceae

As a result of co-evolution between plants and herbivores, related plants often interact with similar communities of herbivores. On individual plants, typically only a subset of interactions is realized. The stochasticity of realized interactions leads to uncertainty of attack on individual plants and is likely to determine adaptiveness of plant defence strategies. Here, we show that across 12 plant species in two phylogenetic lineages of the Brassicaceae, variation in realized herbivore communities reveals a phylogenetic signal in the uncertainty of attack on individual plants. Individual plants of Brassicaceae Lineage II were attacked by a larger number of herbivore species from a larger species pool, resulting in a higher uncertainty of realized antagonistic interactions compared to plants in Lineage I. We argue that uncertainty of attack in terms of realized interactions on individual plants is ecologically relevant and must therefore be considered in the evolution of plant defences.

ecology↗

bioRxiv2019

Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage-specific patterns

The APETALA2 (AP2) subfamily of transcription factors are key regulators of angiosperm root, shoot, flower, and embryo development. The broad diversity of anatomical and morphological structures is potentially associated with the genomic dynamics of the AP2 subfamily. However, a comprehensive phylogenomic analysis of the AP2 subfamily across angiosperms is lacking. We combined phylogenetic and synteny analysis of distinct AP2 subclades in the completed genomes of 107 angiosperm species. We identified major changes in copy number variation and genomic context within subclades across lineages, and discuss how these changes may have contributed to the evolution of lineage-specific traits. Multiple AP2 subclades show highly conserved patterns of copy number and synteny across angiosperms, while others are more dynamic and show distinct lineage-specific patterns. As examples of lineage-specific morphological divergence due to AP2 subclade dynamics, we hypothesize that that loss of PLETHORA1/2 in monocots correlates with the absence of taproots, whereas independent lineage-specific changes of PLETHORA4/BABY BOOM and WRINKLED1 genes in Brassicaceae and monocots point towards regulatory divergence of embryogenesis between these lineages. Additionally, copy number expansion of TOE1 and TOE3/AP2 in asterids is implicated with differential regulation of flower development. Moreover, we show that the genomic context of AP2s is in general highly specialised per angiosperm lineage. Our study is the first to shed light on the evolutionary divergence of the AP2 subfamily subclades across major angiosperm lineages and emphasises the need for lineage-specific characterisation of developmental networks to further understand trait variability. SIGNIFICANCE STATEMENTAPETALA2 transcription factors are crucial regulators of embryogenesis and post-embryonic development in plants. Characterising the genomic dynamics of APETALA2 genes across 107 angiosperms provided evolutionary insights into gene-family and morphological divergence across major angiosperm lineages.

plant biology↗