Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms.

Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 exons, found in 248 single or low-copy nuclear genes, across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate land plants and demonstrate the potential of the data to resolve relationships among both distantly and closely related taxa.

Conclusions: A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

This dataset is the result of targeted enrichment sequencing using a probe set corresponding to 451 nuclear loci.

Details about the dataset and scripts are available in the Breinholt_EtAl_.txt.