Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition

Area of Science:

• Plant evolutionary biology
• Genomics
• Bioinformatics

Background:

• Polyploidization is a key driver of plant evolution.
• High-quality chromosome-level assemblies of polyploid genomes are becoming more common.
• Delineating subgenomes in polyploids, especially without known ancestors, is challenging.

Purpose of the Study:

• To develop and validate a novel method for assigning genome assemblies to subgenomes in polyploid plants.
• To infer the timing of allopolyploidization events.
• To apply the method to complex polyploid genomes, such as the octoploid strawberry.

Main Methods:

• Utilizing long terminal repeat retrotransposons (LTR-RTs) and the serial similarity matrix (SSM) method.
• Identifying subgenome-specific LTRs to facilitate subgenome assignment.
• Validating the SSM approach on known allopolyploid and artificial allotetraploid genomes.

Main Results:

• The SSM method effectively assigns chromosomes to their respective subgenomes.
• The approach accurately identifies subgenome-specific LTRs and infers polyploidization timing.
• Application to the octoploid strawberry genome revealed three distinct allopolyploidization events.

Conclusions:

• The LTR-RT and SSM-based method provides a robust solution for subgenome delineation in polyploids, even without known progenitors.
• This approach enhances our understanding of the evolutionary history of complex polyploid genomes.
• The findings offer new insights into the origin and evolution of the octoploid strawberry genome.