Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Chloroplast (cp) genomes are valuable for plant evolutionary studies, but their resolution power is sometimes limited.
• Integrating cp genome data with nuclear DNA offers a more complete evolutionary picture but often requires separate datasets.
• The Aurantioideae subfamily, including Citrus, presents complex evolutionary relationships.

Purpose of the Study:

• To develop a cost-efficient method for extracting nuclear gene sequences from raw sequencing data using Read2Tree.
• To construct and compare phylogenetic trees based on cp genomes and nuclear DNA from the same raw sequencing data.
• To investigate the causes of discordance between cp and nuclear DNA-based phylogenetic trees in Aurantioideae.

Main Methods:

• Utilized Read2Tree to extract conserved nuclear gene sequences from raw sequencing data.
• Constructed phylogenetic trees using both cp genome data and nuclear DNA sequences.
• Employed an integrative workflow with multiple gene alignments and phylogenomic methods to analyze discordances.

Main Results:

• Nuclear DNA trees derived from Read2Tree were consistent with existing nuclear phylogenies.
• Significant divergences were observed between cp genome-based trees and nuclear DNA-based trees.
• Incomplete lineage sorting was identified as the primary driver of discordance, with introgression also contributing.

Conclusions:

• Read2Tree provides a cost-effective approach for nuclear DNA phylogenetic analysis from raw sequencing data.
• Discordances between cp and nuclear DNA phylogenies in Aurantioideae are mainly due to incomplete lineage sorting and introgression.
• Using the same raw sequencing data for both cp and nuclear DNA analyses enhances understanding of plant evolutionary relationships.