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

ABSTRACT: UNLABELLED: 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.

SUBMITTER: Mandel JR

PROVIDER: S-EPMC4103609 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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

Mandel Jennifer R JR Dikow Rebecca B RB Funk Vicki A VA Masalia Rishi R RR Staton S Evan SE Kozik Alex A Michelmore Richard W RW Rieseberg Loren H LH Burke John M JM

Applications in plant sciences 20140206 2

<h4>Unlabelled</h4><h4>Premise of the study</h4>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. •<h4>Methods and results</h4>We designed a set of sequence capture probes that targ ...[more]

PMID: 25202605

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Project description:PremiseRubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking.MethodsHere, we use publicly accessible genomic resources to identify putatively single-copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent-aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.ResultsWe recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.DiscussionOur probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

Dataset Information

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

Publications

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

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