Home » Next generation sequencing of Zanthoxylum leads to rethink of previous generations of Zanthoxylum

Next generation sequencing of Zanthoxylum leads to rethink of previous generations of Zanthoxylum

Next-generation sequencing using target enrichment reveals that current sectional classifications of Zanthoxylum need revision.

The evolutionary history of Zanthoxylum is more complicated than previously thought. The research by Niklas Reichelt and colleagues shows only two of the five sections of Zanthoxylum are monophyletic. The study indicates that target enrichment, a method that only amplifies part of the genome, can be used to analyse this widespread genus of trees.

Zanthoxylum piperitum. Image: Canva.

Pulling apart a plant’s genome can help scientists work out how it relates to other plants. The closer the genetic similarities, the closer the common ancestor between the plants. Next-generation sequencing has helped botanists work out many of these relationships. Most of these projects haven’t worked with the entire genome. Instead, the scientists focussed on amplifying the parts of the genome that highlight differences in a plant. The focus is valuable to botanists because it requires little DNA meaning that it works well with herbarium samples.

Zanthoxylum, often known as prickly ash or yellowwood, is a genus that could use some clarity. There are around 225 species spread around the tropics of the world. The trees have already had some sequencing done by the same group, and some of the results were puzzling. In the case of the Pacific Zanthoxylum plants, the group appeared to be monophyletic in the plastid dataset but polyphyletic in the nuclear dataset. In plain English, it seems that Pacific Zanthoxylum has a common ancestor, or not, depending on how you look at it.

This time the scientists used target enrichment in Zanthoxylum. They wanted to test if they could use their method to redraw the Zanthoxylum family tree. They could also use it as a comparison to evaluate their previous Sanger sequencing study. Finally, they wanted to see if they could use off-target reads to identify future targets.

The team identified four clades, groups with common ancestors: the African clade, the Z. asiaticum clade, the Asian–Pacific–Australian clade and the American–eastern Asian clade. The team identified the Hawaiian plants as notable as they could be associated with a past hybridisation event.

The results show that Zanthoxylum species need to be reclassified, but it may be too early to do this properly, write Reichelt and colleagues. “A formal proposal of a new sectional or subgeneric classification is premature at this stage, and the taxon sampling, especially regarding Central and South American and Chinese species, needs to be increased significantly in future studies. Nevertheless, the four major clades recognized in our study set the foundation for a subgeneric classification of Zanthoxylum.”


Reichelt N, Wen J, Pätzold C, Appelhans MS. 2021. Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events. Annals of Botany 128: 497–510. https://doi.org/10.1093/aob/mcab092

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