Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq.

Autor: Straub SCK; Department of Biology Hobart and William Smith Colleges 300 Pulteney Street Geneva New York 14456 USA., Boutte J; Department of Biology Hobart and William Smith Colleges 300 Pulteney Street Geneva New York 14456 USA., Fishbein M; Department of Plant Biology, Ecology, and Evolution Oklahoma State University 301 Physical Sciences Stillwater Oklahoma 74078 USA., Livshultz T; Department of Biodiversity, Earth, and Environmental Sciences and the Academy of Natural Sciences Drexel University 1900 Benjamin Franklin Parkway Philadelphia Pennsylvania 19103 USA.
Jazyk: angličtina
Zdroj: Applications in plant sciences [Appl Plant Sci] 2020 Nov 28; Vol. 8 (11), pp. e11400. Date of Electronic Publication: 2020 Nov 28 (Print Publication: 2020).
DOI: 10.1002/aps3.11400
Abstrakt: 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.
(© 2020 Straub et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)
Databáze: MEDLINE
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