Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from...

Area of Science:

• Plant evolutionary biology
• Molecular phylogenetics
• Genomics

Background:

• Phylogenomics is crucial for understanding evolutionary relationships.
• The use of concatenated orthologous genes under diverse selective pressures for phylogenomic reconstruction is debated.

Purpose of the Study:

• To investigate RNA sequencing efficiency for resolving closely related species within Pedicularis sect. Cyathophora.
• To assess the impact of gene selection and concatenation strategies on phylogenetic accuracy.

Main Methods:

• Sequencing of flower transcriptomes for all species in Pedicularis sect. Cyathophora and two outgroups.
• Identification and concatenation of 41 conserved nuclear genes and 1553 orthologous groups (OGs) into five datasets.
• Phylogenetic reconstruction using varying gene numbers and orthologous groups.

Main Results:

• Phylogenetic analyses using five distinct datasets consistently resolved interspecific relationships within Pedicularis sect. Cyathophora.
• Robust phylogenetic reconstruction with maximal support was achieved using at least 20 single-/low-copy nuclear genes or 25 OGs.
• The study demonstrated that orthologous groups under different selective pressures can be concatenated for reliable phylogenomic analysis.

Conclusions:

• RNA sequencing provides an efficient method for reconstructing interspecific relationships in rapidly radiating, non-model plant groups.
• The findings support the concatenation of orthologous groups with varying selective pressures for robust phylogenomic reconstruction.
• This study establishes a reliable phylogenomic framework for Pedicularis sect. Cyathophora, aiding future evolutionary studies.