A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae
Monique Romeiro-Brito1, Milena Cardoso Telhe1, Danilo Trabuco Amaral1,2
1Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, SP, Brazil.
Genes
|April 23, 2022
Summary
A new probe set, Cactaceae591, resolves phylogenetic relationships in cacti. Targeting nuclear regions is key for understanding cactus family evolution and phylogeography.
Area of Science:
- Botany
- Molecular Biology
- Evolutionary Biology
Background:
- Molecular phylogenies have advanced understanding of Cactaceae systematics, biogeography, and diversification.
- Phylogenetic relationships within major cactus groups remain largely unresolved due to limitations in molecular markers.
Purpose of the Study:
- To develop a novel molecular marker set for resolving phylogenetic relationships within the Cactaceae family.
- To assess the utility of this marker set for phylogeographic studies at inter- and intraspecific levels.
Main Methods:
- Exploration of genome and transcriptome assemblies to identify orthologous regions in Cactoideae.
- Development of the Cactaceae591 probe set targeting nuclear coding and noncoding regions across Cactaceae subfamilies.
- Sampling of inter- and intraspecific variation to evaluate phylogeographic potential.
Main Results:
- Successfully identified and targeted 547 orthologous regions per sample using the Cactaceae591 probe set.
- Demonstrated the critical role of noncoding nuclear regions in resolving inter- and intraspecific relationships.
- Cactaceae591 integrates with existing angiosperm and Cactaceae markers, facilitating combined phylogenetic analyses.
Conclusions:
- The Cactaceae591 probe set is effective for resolving cactus phylogeny and phylogeography.
- Noncoding nuclear DNA is essential for high-resolution phylogenetic studies in Cactaceae.
- Coalescent-based species tree methods are recommended for accurate phylogenetic inference with this dataset due to incomplete lineage sorting.
