Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches

Abstract Single and low copy nuclear genes offer a larger number of, and more rapidly evolving, characters than the chloroplast and nuclear ribosomal gene sequences that have dominated plant phylogenetic studies to date. Until recently, only one or a few low copy nuclear gene markers were included in such studies. Now, the rapid adoption of “next generation sequencing” (NGS) techniques offers simpler and cheaper access to hundreds of, and not just tens of, coding and noncoding DNA regions. In this review, we describe the most commonly‐used NGS methods available for accessing nuclear genes and discuss many NGS case studies that have been published in the last two to three years. These approaches include whole genome sequencing to target microsatellites, transcriptome sequencing, Exon‐Primed Intron‐Crossing sequencing (EPIC), targeted enrichment (or sequence capture), RAD sequencing (RAD‐Seq, including genotyping‐by‐sequencing or GBS), and genome skimming. We also discuss some of the challenges to, and posed by, the NGS approaches.