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

Shannon C K Straub1, Julien Boutte1, Mark Fishbein2

  • 1Department of Biology Hobart and William Smith Colleges 300 Pulteney Street Geneva New York 14456 USA.

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Summary

This study developed a targeted sequencing probe set for the Apocynaceae plant family, enabling advanced population genomics and phylogenomics research. The new method successfully identified nuclear genes for robust phylogenetic analysis.

Keywords:
ApocynaceaeHyb‐Seqdogbanegenome reductionlow‐copy nuclear genesmilkweedphylogenomicstargeted sequencing

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Area of Science:

  • Botany and Plant Science
  • Genomics and Bioinformatics
  • Evolutionary Biology

Background:

  • The Apocynaceae family, a major group of flowering plants, lacks sufficient genomic resources for detailed studies on plant-insect interactions.
  • Secondary metabolites in Apocynaceae are key to understanding plant-insect interactions, but genomic limitations hinder research.
  • Target capture sequencing offers a solution for genome reduction in non-model organisms like Apocynaceae.

Purpose of the Study:

  • To develop and validate a targeted sequencing approach for generating nuclear genomic data in Apocynaceae.
  • To assess the utility of targeted sequencing for phylogenetic inference and population-level genetic studies within the family.
  • To create a valuable genomic resource for the scientific community studying Apocynaceae.

Main Methods:

  • Designing probes for targeted sequencing of putatively single-copy nuclear genes using Apocynaceae transcriptomes.
  • Sequencing targeted genes to evaluate probe design success, genetic variation, and phylogenetic utility.
  • Utilizing coalescent-based species tree analysis to infer evolutionary relationships.

Main Results:

  • Successfully identified 835 single-copy nuclear genes suitable for phylogenomics from 853 candidates.
  • Confirmed the monophyly of Apocynaceae subfamilies and resolved relationships within the genus *Apocynum*.
  • Discovered numerous single-nucleotide polymorphisms in *Elytropus chilensis*, valuable for population genetics.

Conclusions:

  • The developed Hyb-Seq probe set is a powerful tool for advancing Apocynaceae research.
  • This resource will facilitate studies ranging from population genomics to broad-scale phylogenomics.
  • Community adoption of this probe set will accelerate discoveries in Apocynaceae biology.