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Journal article
Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq
Applications in plant sciences, v 8(11), pp e11400-n/a
Nov 2020
PMID: 33304663
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Premise
Apocynaceae is the 10th largest flowering plant family and a focus for study of plant–insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non‐model taxa, such as Apocynaceae.
Methods
Transcriptomes were used to design probes for targeted sequencing of putatively single‐copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny.
Results
From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent‐based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genus Apocynum. Intraspecific comparison of Elytropus chilensis individuals revealed numerous single‐nucleotide polymorphisms with potential for use in population‐level studies.
Discussion
Community use of this Hyb‐Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
Metrics
Details
- Title
- Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq
- Creators
- Shannon C. K. Straub - Department of Biology Hobart and William Smith Colleges 300 Pulteney Street Geneva New York14456USAJulien Boutte - Department of Biology Hobart and William Smith Colleges 300 Pulteney Street Geneva New York14456USAMark Fishbein - Oklahoma State UniversityTatyana Livshultz - Drexel University
- Publication Details
- Applications in plant sciences, v 8(11), pp e11400-n/a
- Publisher
- Wiley
- Number of pages
- 9
- Grant note
- National Science Foundation (1655223/1655553; 1457473/1457510) Drexel University
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES)
- Web of Science ID
- WOS:000593071400001
- Scopus ID
- 2-s2.0-85096843363
- Other Identifier
- 991019167680704721
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InCites Highlights
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Plant Sciences