Data from: Comparison of taxon-specific versus general locus sets for targeted sequence capture for 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 having orthologs in
large clades of plants. Methods: We identify and compare a taxon-specific
locus set and three general locus sets (COSII, APVO SSC, PPR) 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 dataset produced the best
supported tree, but all datasets showed improved resolution over previous
non-sequence capture datasets. Discussion: General loci can be a useful
source of sequence capture targets, especially if multiple genomic
resources are not available for a taxon.