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

Abstract

Premise of the StudyTargeted 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.MethodsWe 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.ResultsThe 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.DiscussionGeneral locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

“…This is comparable to 1362 bp for a Heuchera L. kit (Folk et al., ), 1667 bp for a Leguminosae kit (Vatanparast et al., ), and ~1645 bp for a Euphorbia L. kit (Villaverde et al., ). However, average target length was shorter (820 bp) for Buddleja L.‐specific locus sets compared to three different non‐taxon‐specific locus sets (1267 bp; Chau et al., ). In contrast, the average target length for the universal Angiosperm‐353 and Angiosperm v.1 kits was 738 bp and 343 bp, respectively.…”

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

“…Despite the fact that the probes were designed for CDC Redberry, a Canadian cultivar, the low specificity of the probes allows this method to be used for wild lentil species as well. Probes with low specificity have been successfully utilized in studies on divergent taxa, but they usually produce fewer variants than the taxon‐specific probes (Bragg et al., 2016; Chau et al., 2018). However, in our stringently filtered data set, we were able to identify 6.5 million variants across the initial 38 samples tested.…”

Methods for exploring the plant tree of life

“…Chau et al. () and Vatanparast et al. () provide reviews of different methods for sequence capture, focusing on marker selection.…”

“…Chau et al. () focus on collecting data to resolve rapid radiations, comparing the efficiency of custom‐designed, taxon‐specific probe sets to more universal sets of probes (i.e., conserved ortholog set [COSII], shared single‐copy nuclear genes [APVO SSC], and pentatricopeptide repeats [PPR]) that are designed to work across a broad array of angiosperms. Chau et al.…”

“…Chau et al. () find that although targeting taxon‐specific markers may not always be necessary, in their case, the taxon‐specific set of loci did provide better assemblies and a better‐supported phylogeny within Buddleja L. (Scrophulariaceae) than those obtained with universal probe sets. For researchers wishing to explore the use of custom‐designed probe sets, Vatanparast et al.…”