Aarhus Universitets segl

Plant Phylogenomics and Herbariomics

Using genomic techniques and natural history collections to reconstruct the plant Tree of Life

Phylogenetic research is currently being revolutionised by new molecular methods, and we are trying to be at the forefront of this movement.

Traditionally, Tree of Life research has had to rely on focused sequencing of few DNA regions, using techniques that were time-consuming and required high-quality DNA samples. Being dependent on these techniques, our knowledge the plant Tree of Life remained limited in two ways: few DNA regions are not always sufficient to accurately disentangle evolutionary history, and many species for which only poor-quality DNA could be obtained remained out of reach. Both these limitations are now increasingly being removed by phylogenomics.

New techniques, such as sequence capture, allow sequencing many DNA regions at the same time, representing the evolutionary history of the entire genome much more accurately than traditional approaches. At the same time, these new methods inherently lend themselves to working with poor quality (i.e., highly fragmented) DNA, unlocking countless specimens in natural history collections for Tree of Life research. In plants, this new opportunity is called "herbariomics".

We have been involved in the development of a sequence capture approach (Johnson et al. 2018) and testing it on specimens of different quality (Brewer et al. 2019). We are associated with to the Plant and Fungal Trees of Life (PAFTOL) project at the Royal Botanic Gardens, Kew, which generates new sequence capture data for all genera of flowering plants, and the Palm Phylogeny Working Group, which does the same for all species of the palm family (Arecaceae). Many of our projects involve phylogenomics of smaller lineages, such as the genera Maesa (Primulaceae) and Saxifraga (Saxifragaceae) and various palm lineages.

Group members involved: Peter Petø, Pirada Sumanon, Angelo Moerland, Ben Kuhnhäuser, Sebastián Escobar, Maya Schrödl, Wolf Eiserhardt

Key collaborators: The PAFTOL team (Royal Botanic Gardens, Kew); Sidonie Bellot (Royal Botanic Gardens, Kew)

Read more:

  • Brewer GE, Clarkson JJ, Maurin O, Zuntini AR, [...] Eiserhardt WL, [...] Forest F, Baker WJ (2019) Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms. Frontiers in Plant Science 10:1102.
  • Johnson MG, Pokorny L, Dodsworth S, [...] Eiserhardt WL, [...] Baker WJ, Wickett NJ (2018) A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Systematic Biology 68, 594-606.