Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in...

Area of Science:

• Plant genomics
• Organellar DNA evolution
• Molecular evolution

Background:

• Repeats are known to mediate genome rearrangements and recombination in plant organellar genomes.
• The precise impact of repeat accumulation on sequence and structural evolution remains debated.

Purpose of the Study:

• To investigate the relationship between repeats, nucleotide substitution rates, and structural variations in 75 Plantago plastomes.
• To understand the role of repeats in driving evolutionary rates and genome instability.

Main Methods:

• Analysis of 75 Plantago plastomes.
• Long-read sequencing to detect substoichiometric shifting.
• Examination of nucleotide substitution rates and structural variations, including rearrangements and inversions.

Main Results:

• Extensive repeat accumulation correlated with significant rearrangements and inversions in large inverted repeats (IRs), indicating repeat-mediated rearrangement hotspots.
• Infrequent recombination events linked to repeats potentially caused substoichiometric shifting.
• Repeats were associated with elevated evolutionary rates via localized hypermutation and DNA repair processes.
• Loci translocating into IRs showed decreased nucleotide substitution rates, suggesting biased gene conversion.

Conclusions:

• Repeats significantly influence the structural evolution and stability of plant plastid genomes.
• Potential dysfunction in nuclear genes controlling DNA replication, recombination, and repair may drive organellar genome evolution in Plantago, paralleling mitogenome changes.
• These findings are crucial for understanding rapid evolution in plant organellar lineages.