APPLICATION ARTICLE Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq Shannon C. K. Straub1,4 , Julien Boutte1, Mark Fishbein2 , and Tatyana Livshultz3 Manuscript received 1 July 2020; revision accepted 12 September PREMISE: Apocynaceae is the 10th largest flowering plant family and a focus for study of 2020. plant–insect interactions, especially as mediated by secondary metabolites. However, it has 1 Department of Biology, Hobart and William Smith Colleges, 300 few genomic resources relative to its size. Target capture sequencing is a powerful approach Pulteney Street, Geneva, New York 14456, USA for genome reduction that facilitates studies requiring data from the nuclear genome in non- 2 Department of Plant Biology, Ecology, and Evolution, Oklahoma model taxa, such as Apocynaceae. State University, 301 Physical Sciences, Stillwater, Oklahoma 74078, USA METHODS: Transcriptomes were used to design probes for targeted sequencing of putatively 3 Department of Biodiversity, Earth, and Environmental Sciences single-copy nuclear genes across Apocynaceae. The sequences obtained were used to assess and the Academy of Natural Sciences, Drexel University, 1900 the success of the probe design, the intrageneric and intraspecific variation in the targeted Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103, USA genes, and the utility of the genes for inferring phylogeny. 4Author for correspondence:
[email protected] RESULTS: From 853 candidate nuclear genes, 835 were consistently recovered in single Citation: Straub, S. C. K., J. Boutte, M. Fishbein, and T. Livshultz. copy and were variable enough for phylogenomics. The inferred gene trees were useful for 2020. Enabling evolutionary studies at multiple scales in coalescent-based species tree analysis, which showed all subfamilies of Apocynaceae as Apocynaceae through Hyb-Seq.