Biology subjects

Verhoeven, K. J.

Publications and source records attributed to Verhoeven, K. J..

3 recordsLinked to original sources

bioRxiv2025

Universal Hyb-Seq kits capture considerable intraspecific variation: Less is more in herbarium-inclusive molecular ecology

Target capture sequencing has enhanced the study of plant evolution and molecular ecology, particularly through the access to degraded DNA from herbarium specimens. Universal "off-the-shelf" kits, such as Angiosperms-353, are cheap and readily available but are considered to expose insufficient variation below the species level, because they are designed to target highly conserved regions. However, this remains to be tested in a direct comparison with customised approaches below the species level. In this study, near-identical genotypes from both herbarium and fresh material of the common dandelion (apomictic lineages in Taraxacum officinale F.H.Wigg.) are characterised with customised and universal approaches of target capture sequencing. An RNA-bait panel was designed to capture (i) highly variable loci normally obtained with a Genotyping-by-Sequencing (GBS) approach customised for dandelions; (ii) custom selected genes with potential for environmental adaptation, likely to harbour intraspecific genetic variation; (iii) conserved exons from universal kits (Angiosperms-353; Compositae-COS). Although exons from universal kits yield considerably less intraspecific genetic variation than both customised approaches, they still provided sufficient genetic variation to discriminate between near-identical genotypes of the same apomictic lineage. Given that universal kits save time, money, and the need for genomic reference data, this approach is recommended to increase the number of samples under budgetary constraints while still capturing considerable levels of intraspecific genetic variation.

genomics↗

bioRxiv2023

Some like it hot: adaptation to the urban heat island in common dandelion.

The Urban Heat Island Effect (UHIE) is a globally consistent pressure on species living in cities. Rapid adaptation to the UHIE may be necessary for urban wild flora to persist in cities, but experimental evidence is lacking. Here, we report the first evidence of genetic differentiation in a plant species in response to the UHIE. We collected seeds from common dandelion (Taraxacum officinale) individuals along an urban-rural gradient in the city of Amsterdam (The Netherlands). In common-environment greenhouse experiments, we assessed the effect of elevated temperatures on plant growth and the effect of vernalisation treatments on flowering phenology. We found that urban plants accumulate more biomass at higher temperatures and require shorter vernalisation to induce flowering compared to rural plants. Differentiation was also observed between different intra-urban subhabitats, with park plants displaying a higher vernalisation requirement than street plants. Our results show strong differentiation between urban and rural dandelions in temperature-dependent growth and phenology, consistent with adaptive divergence in response to the UHIE. Rapid adaptation to the UHIE may be a potential explanation for the widespread success of dandelions in urban environments. Summary statementThe urban heat island effect (UHIE) is the most prominent and globally consistent characteristic of environmental change due to urbanisation, severely impacting human populations in cities as well as the cohabiting wildlife. Despite the profoundly mitigating effect of vegetation on urban heat, evidence for plant adaptation to the UHIE has been lacking. Here we provide the first experimental evidence to date, demonstrating adaptation in urban dandelions in response to elevated temperatures, similar to the UHIE. We furthermore show an urban-rural differentiation in flowering response to shorter vernalisation times (cold winter period to activate the onset of flowering in early spring). Given the predominantly asexual apomictic mode of reproduction in dandelions, this evolution is likely the result of environmental filtering on a diverse population of clonal genotypes. We conclude that plant adaptation to the UHIE exists and recommend future studies to contrast our findings with those in outcrossing sexual plant systems. Studies of urban heat adaptation can bring impactful contributions to building climate change-resilient environments and plants should be an integral part of this research.

plant biology↗

bioRxiv2022

High-resolution methylome analysis in the clonal Populus nigra cv. 'Italica' reveals environmentally sensitive hotspots and drought-responsive TE superfamilies

ABSTRACT/SUMMARYO_LIDNA methylation is environment-sensitive and can mediate plant stress responses. In long-lived trees, changing environments might cumulatively shape the methylome landscape over their lifetime. However, because high-resolution methylome studies usually focus on single environments, it remains unclear to what extent the methylation responses are generic or stress-specific, and how this relates to their long-term stability. C_LIO_LIHere, we studied the methylome plasticity of a single poplar genotype, Populus nigra cv. Italica. Adult poplar trees with diverse environmental histories were clonally propagated, and the ramets exposed to experimental cold, heat, drought, herbivory, rust infection and salicylic acid treatments. Then, we identified and compared stress-induced vs. naturally occurring DNA methylation changes using whole genome bisulfite sequencing data. C_LIO_LIMethylation changes mainly targeted transposable elements and when occurring in CG/CHG contexts, the same regions were often affected by multiple stresses, indicating a generic response. Drought triggered a unique CHH hypermethylation response in transposable elements, affecting entire superfamilies and often occurring near drought-responsive genes. Stress-induced methylation variation in CG/CHG contexts showed striking overlap with methylation differences observed between trees from distinct geographical locations. C_LIO_LIAltogether, our results indicate that generic methylome stress responses can persist as epialleles in nature while some environments trigger more transient but large and specific responses, with possible functional consequences. C_LI

genomics↗