A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae

Abstract

• Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and 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.• Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family.• Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…A phylogenomic approach targeting thousands of independently evolved nuclear loci may be the only way to assess the current taxonomy of this group, and dissect the roles of hybridization and introgression in the origin and rapid diversification of this insular lineage. Phylogenomic methods based on markers identified from, e.g., restriction site associated DNA sequencing (RADseq) (Cruaud et al, 2014;Eaton and Ree, 2013;Smith et al, 2014), targeted enrichment of ultraconserved elements (UCEs) or conserved ortholog sequences (COS) (Mandel et al, 2014;Smith et al, 2014), and RNA-Seq (Wen et al, 2013;Wickett et al, 2014) could be suitable methods to resolve Hawaiian mint relationships. However, these approaches are also associated with challenges, including accurately inferring orthology in high polyploid plants, slow mutation rates in exonic regions, which may be too low to resolve recent radiations (Giarla and Esselstyn, 2015), and the need to obtaining high quality RNA and DNA.…”

Using phylogenomics to resolve mega‐families: An example from Compositae

“…Sequence capture was performed using a custom probe set, MyBaits designed by MYcroarray (Ann Arbor, Michigan, USA) and described in Mandel et al (2014). DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent, Santa Clara, California, USA), quantified using a Qubit 2.0 Fluorometer (Life Technologies, Grand Island, New York, USA), pooled, and sequenced on either two lanes of an Illumina HiSeq 2000 sequencer (2 Â 100 bp read length) or one run of the Illumina MiSeq sequencer (2 Â 250 bp read length).…”

“…All of these studies are hampered by the unresolved areas of the base tree. Mandel et al (2014) previously demonstrated the utility of sequence capture and NGS for resolving relationships within the family. Here we expand upon that previous work by considering multi-copy genes in our data set using a clustering approach, during orthology detection prior to gene-tree phylogenetic analysis.…”

“…Here we expand upon that previous work by considering multi-copy genes in our data set using a clustering approach, during orthology detection prior to gene-tree phylogenetic analysis. Instead of excluding taxa with greater than one match for a particular locus (as in Mandel et al, 2014), all copies are analyzed by clustering these into "genes within genes." Using this output, a network approach is applied to begin to identify and understand gene tree incongruence and the complex dynamics of plant nuclear gene families.…”

“…These COS probes were developed by identifying homologues to Arabidopsis single copy genes in three Compositae (safflower, sunflower, lettuce; see Mandel et al, 2014 for a detailed description of the development). Because the sunflower genome is more than 81% repetitive (Staton et al, 2012), much of its genome (likely also for many other species of Compositae) is not amenable to phylogenetic analysis, gene target enrichment is one way to capture only potentially phylogenetically informative regions of the genome.…”