Structural conservation and SSR-driven divergence in Lepidium chloroplast genomes: balancing genomic stability with adaptive plasticity.

Abstract

The chloroplast genomes of 13 Lepidium species were analyzed to explore how structural conservation and SSR (Simple Sequence Repeat) dynamics balance genomic stability with adaptive divergence. While genome size and GC content remained highly conserved, reflecting strong functional constraints on photosynthetic machinery, repetitive elements exhibited striking lineage-specific diversity. Mid-length, AT-rich SSRs dominated across species, with conserved motifs (e.g., pentanucleotide TCCAT) likely underpinning structural integrity. In contrast, clade-specific innovations, such as absent octanucleotide repeats in Lepidium cordatum and Lepidium draba or unique pentanucleotide expansions, highlight adaptive plasticity in non-essential regions. These findings reveal a dual evolutionary strategy: chloroplast genomes maintain core functions through conserved architecture while permitting localized SSR-driven innovations, potentially enhancing ecological resilience. This interplay underscores how genomic stability and plasticity coexist to enable adaptation in dynamic environments, offering new insights into the evolutionary mechanisms shaping plant organelle genomes.