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Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae)
Seth D Musker1,2, Nicolai M Nürk2, Michael D Pirie3
1Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa University of Bayreuth Bayreuth Germany.
Phytokeys
|January 27, 2025
Summary
Developing a custom target set for plant phylogenomics, particularly for the Erica genus, significantly improves phylogenetic resolution. This approach enhances data informativeness and intron recovery, overcoming limitations of universal gene sets for complex evolutionary studies.
Area of Science:
- Plant phylogenetics and phylogenomics
- Genomic data acquisition and analysis
Background:
- Target capture sequencing (Hyb-Seq) is a standard method in plant phylogenomics, enabling the study of numerous genomic regions (loci).
- A major challenge is selecting appropriate loci, especially for non-model organisms lacking pre-existing genomic resources.
- Existing universal gene sets may lack sufficient phylogenetic signal for rapidly radiating or complex plant groups.
Purpose of the Study:
- To design a custom target capture set for Erica phylogenomics to maximize phylogenetic informativeness and minimize paralogy.
- To ensure the universality of the target set by incorporating genes from the widely used Angiosperms353 set.
- To assess the performance of the custom target set in terms of gene recovery, information content, and intron recovery.
Main Methods:
- Designed a custom target set of over 300 genes for Erica, including conserved genes from the Angiosperms353 set.
- Applied target capture sequencing to approximately 90 Erica species and related outgroups (Calluna, Daboecia, Rhododendron).
- Analyzed data for recovery rates, parsimony informative sites, and Quartet Internode Resolution Probability (QIRP), correlating QIRP with intron content.
Main Results:
- Achieved excellent target recovery rates across diverse Erica species and outgroups.
- Demonstrated high phylogenetic information content, with QIRP positively correlated with intron content.
- Found that including introns directly in target sets substantially improved intron recovery compared to exon-flanking bycatch.
Conclusions:
- Building custom target sets is highly valuable for overcoming limitations of universal sets in plant phylogenomics.
- The developed Erica-specific target set effectively maximizes phylogenetic informativeness and intron recovery.
- Open-source tools are provided to facilitate the replication of this approach for other plant groups.
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