Reprint of: Using nuclear gene data for plant phylogenetics: Progress and prospects

The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.

► Twenty currently used low copy number nuclear genes are discussed.
► Next generation sequencing (NGS) produces many phylogenetically useful characters.
► NGS also produces data relevant to the evolution of gene expression and polyploidy.