Biology subjects

Bouwmeester, K.

Publications and source records attributed to Bouwmeester, K..

3 recordsLinked to original sources

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↗