Biology subjects

Woudstra, Y.

Publications and source records attributed to Woudstra, Y..

6 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↗

bioRxiv2025

Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids)

Background and AimsWith >700 species, Aloe and its generic kin (alooids) are a morphologically diverse group of succulent plants with a wide range across Africa, Madagascar and the Arabian Peninsula. Species such as Aloe vera and A. ferox are cultivated at scale for natural products, whole foods, and cosmetics. Despite substantial -taxonomy contributions, infrageneric classification of Aloe has remained unresolved. Molecular systematics has been compromised by the lack of informative characters in standard markers and high costs of obtaining informative nuclear loci from large genomes (e.g. >15 Gbp); and the difficulty of obtaining quality DNA extractions from material of known provenance. Here these constraints are overcome with target capture sequencing that allows cost-effective sequencing of informative low-copy nuclear loci and unlocks genetic resources from preserved specimens in herbaria as well as silica-dried tissues. MethodsUsing a custom kit for alooids, 189 nuclear loci were sequenced in 294 species, including 50 herbarium specimens, to build a new phylogenomic framework for the big genus Aloe and 11 closely related genera in the alooid clade. Available taxonomic classifications for Aloe sensu stricto were contrasted against the obtained topology in an effort to stabilise taxonomy. Genus-level representations of the family Asphodelaceae were sequenced with the same tool. Key resultsThe new phylogenomic framework demonstrates the monophyly of the alooids and confirms recent classifications in which smaller genera (Aloidendron, Aloiampelos, Aristaloe, Gonialoe, Kumara) are separated. Strong geographic patterns in the Aloe phylogeny are contrasted by less obvious phylogenetic structure in habit (growth form), and vegetative or reproductive morphology that are mainstays of -taxonomy. ConclusionRepeated incidents of adaptive radiation and niche specialisation appear to underlie species diversity in Aloe. This study illustrates the power of combined (nuclear) phylogenomic and -taxonomic inference, including the utility of herbarium genomics, in resolving the systematics of big genera. Lay summaryThe alooids are a group of >700 succulent plants, such as Aloe vera. Testing their taxonomy with genetics is difficult as Aloe genomes are large and very similar between species. A targeted approach was used to classify alooids with highly variable nuclear genes in {+/-}300 species. The evolutionary relationships of alooids are determined principally by geographic distribution patterns, rather than plant morphology or flower shape.

evolutionary biology↗

bioRxiv2024

Assessing male reproductive investment in Papaveraceae using flow cytometry reveals lineage-specific trajectories to pollen-to-ovule ratio reduction

Male reproductive investment, in particular pollen production, is a crucial and ecologically relevant component of a plants phenotype and reproductive success. Its evolutionary trajectory, however, remains understudied, partly due to a lack of convenient methods to assess it. We developed a protocol for pollen quantification by flow cytometry and applied it to 107 flowers from 38 Papaveraceae species differing widely in floral traits (e.g., floral symmetry, stamen number), pollination syndromes (e.g., wind and insect pollination) and reproductive systems (e.g., degree of autogamy). We phylogenetically tested whether pollen number evolved in association with ovule, carpel, stamen and flower numbers per inflorescence, and if there were interacting effects between floral symmetry and/or self-compatibility with pollen and ovule production. Compared to manual counts, results using flow cytometry were similar, but much faster to obtain and more precise. Pollen and ovule numbers per flower varied > 39,000x and > 550x, respectively, among species. Pollen production correlated positively with ovule, carpel and stamen numbers. Lineage-specific trajectories to pollen-to-ovule ratio reduction (to values < 300) are observed. One involved increased female investment in ruderal species belonging to the subfamily Papaveroideae, while the other occurs through decreased male investment and is associated with the evolution of floral traits towards greater specialisation. The impact of reproductive systems on male and female investment is limited to ovule production in non-actinomorphic flowers. Taken together, these results revealed that the evolutionary associations between reproductive systems, floral traits, and pollen and ovule production are lineage-specific. Given the profound contrasts at the subfamily level of Papaveraceae, broader surveys across the diversity of flowering plants are clearly needed to better understand factors driving the evolution of reproductive investment. Such studies will certainly be facilitated by our new high-throughput pollen counting method outlined here.

plant biology↗

bioRxiv2024

An updated DNA barcoding tool for Aloe vera and related CITES-regulated species

DNA barcoding has revolutionised the identification of illegally traded material of endangered species as it overcomes the lack of resolution encountered with morphological identification. Nonetheless, in recently evolved and highly diverse clades, such as the relatives of Aloe vera, the lack of interspecific sequence variation in standardised markers compromises the barcoding efficacy. We present a new DNA barcoding tool using 189 nuclear markers, optimised for aloes (Asphodelaceae, Alooideae). We built a comprehensive sequence reference dataset from taxonomically verified sources for >300 species and validated its reliability for identification using phylogenomic inference. Seven anonymised samples from verified botanical collections and ten plants seized at London Heathrow Airport were correctly identified to species level, including a critically endangered species from Madagascar. Commercially purchased samples were confirmed to be the species as advertised. An accurate, reliable DNA barcoding method for aloe identification introduces new assurance to regulatory processes for endangered plants in trade.

genomics↗

bioRxiv2023

Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plants resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. Plain language summaryNLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.

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↗