Ongoing structural changes highlight the dynamic nature of chloroplast genomes

Area of Science:

• Plant genomics
• Evolutionary biology
• Bioinformatics

Background:

• High-throughput sequencing advances chloroplast genome research.
• Standard methods may miss crucial structural evolutionary signals.

Purpose of the Study:

• Develop a rapid bioinformatic strategy to detect subtle structural rearrangements in chloroplast genomes.
• Investigate plastome evolution in the Aurantioideae subfamily.

Main Methods:

• Reanalysis of existing shallow whole-genome sequencing data.
• Development of a novel bioinformatic pipeline for detecting structural variations.

Main Results:

• Identified the emergence of inverted repeat pairs destabilizing the chloroplast genome.
• Discovered a ~22 kb inversion in the large single-copy region, creating two genomic configurations.
• Uncovered structural heteroplasmy maintained since the early Miocene, with isoforms shifting dominance via genetic drift.

Conclusions:

• Chloroplast genomes exhibit dynamic and unstable evolutionary transitions.
• Gradual structural changes, not discrete events, represent intermediate stages of plastome evolution.
• Structural transitions are a key mechanism driving chloroplast genome diversification.