Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics

Premise of the Study Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single‐copy nuclear loci. Most published studies in plants have used taxon‐specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single‐copy and have orthologs in large clades of plants. Methods We identify and compare a taxon‐specific locus set and three general locus sets (conserved ortholog set [ COSII ], shared single‐copy nuclear [ APVO SSC ] genes, and pentatricopeptide repeat [ PPR ] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results The taxon‐specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon‐specific and PPR loci had the highest average variability. The taxon‐specific data set produced the best‐supported tree, but all data sets showed improved resolution over previous non‐sequence capture data sets. Discussion General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.