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Abstract Detail

Recent Topics Posters

Straub, Shannon [1], Boutte, Julien [1], Fishbein, Mark [2], Livshultz, Tatyana [3].

A New Probe Set for Targeted Enrichment of Nuclear Genes Across Apocynaeae.

Due to multiple ancient rapid radiations, the phylogeny of Apocynaceae has been difficult to infer. Thus far, even with the large data sets afforded by whole plastome sequencing, resolution of the backbone has been elusive. In order to resolve the phylogeny of Apocynaceae, a large amount of data from the nuclear genome will be required. Towards this end, transcriptomes from five species of Apocynaceae were used to identify 853 putatively single copy genes and design probes to target them. Probes were tested for target enrichment success in 14 species of Apocynaceae spanning the diversity of the family and including representatives of four of the five subfamilies, as well as a representative of Gelsemiaceae, another family of Gentianales. Enriched libraries were sequenced using Illumina technology. Gene sequences were obtained using HybPiper, yielding a final set of 837 genes that assembled well across the family. Gene sequences were aligned with Mafft. Phylogenetic analyses to infer gene trees were conducted in IQTree, and a species tree was obtained using ASTRAL. The species tree fully resolved subfamily and tribal relationships with posterior probabilities ranging from 0.99 to 1. In general the topology agreed with previously recovered relationships in the family. However, a striking difference was the monophyly of Rauvolfioideae, which has been recovered as a basal grade in numerous traditional molecular phylogenetics studies and analyses of whole plastome data. The successful targeting of single-copy nuclear genes demonstrated in this study and availability of the probe sequences to the research community will facilitate progress in resolving the phylogeny of Apocynaceae.

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1 - Hobart and William Smith Colleges, Department of Biology, 300 Pulteney St., Geneva, NY, 14456, USA
2 - Oklahoma State University, Department of Plant Biology, Ecology, and Evolution, 301 Physical Sciences, Stillwater, OK, 74078, USA
3 - Drexel University, Biodiversity Earth and Environmental Sciences, Academy Of Natural Sciences Of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, United States

target enrichment
single-copy nuclear genes

Presentation Type: Recent Topics Poster
Session: P, Recent Topics Posters
Location: Grand Ballroom - Exhibit Hall/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 5:30 PM
Number: PRT030
Abstract ID:1326
Candidate for Awards:None

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