Sequence Capture for Compositae Phylogenetics.

The Compositae (Asteraceae) are a large (25,000-33,000 species) and diverse family of plants that include critical members of threatened ecosystems and species of economic importance, as well as invasives. The most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses and the testing of hypotheses related to phenotypic evolution across the family. Specifically, we designed a set of sequence capture probes that target conserved orthologous sequences from existing sunflower, lettuce, and safflower genomic resources and optimized protocols for target enrichment. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to a set of 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci along with the successful reconstruction of known phylogenetic relationships across the family.