@ARTICLE{TreeBASE2Ref27902, author = {John Hoi Chau and Wolfgang A. Rahfeldt and Richard G Olmstead}, title = {Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics}, year = {2017}, keywords = {Buddleja; hybrid enrichment; Lamiales; PPR genes; Scrophulariaceae; single-copy nuclear genes}, doi = {}, url = {http://}, pmid = {}, journal = {Applications in Plant Sciences}, volume = {}, number = {}, pages = {}, abstract = {Premise of the study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci when used with multiplexing and high-throughput sequencing platforms. Most published studies in plants use taxon-specific target locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from sets of 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 for Buddleja (Scrophulariaceae). 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 greatest quantity of target loci. Assembly success was high for all locus sets in Buddleja samples, but for outgroups general locus sets had substantially greater assembly success. Loci in the taxon-specific and PPR locus sets had the highest variability. The taxon-specific sequence dataset produced the best supported tree. Discussion: We suggest that researchers consider including general locus sets as sequence capture targets for phylogenomic work, especially if genomic resources are not available for their clade of interest. } }

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