Repetitive sequence landscapes provide insights into the proliferation and reduction of pericentromeric/centromeric repeats in the genus Glycyrrhiza

Repetitive DNA sequences are a major component of plant genomes and play crucial roles in regulating gene expression, maintaining genome stability, driving genome evolution and facilitating chromosome pairing and segregation. The medicinal licorice genome contains a high proportion of repetitive sequences (61.7%); however, the structure, composition, and evolutionary divergence of these sequences within the Glycyrrhiza genus remain poorly understood. In this study, we determined the repeat landscape of Glycyrrhiza uralensis using a de novo assembled approach integrated with fluorescence in situ hybridization (FISH). FISH analysis of 25 representative repeats revealed that certain highly repetitive sequences, such as rDNA and pericentromeric/centromeric-specific repeats, were either underestimated or misassembled in the current genome assembly. Comparative cytogenetic analyses across seven licorice species revealed that Gly218 (26S rDNA) and Gly277 (5S rDNA) maintained a conserved evolutionary pattern within the genus Glycyrrhiza. Genomic and FISH analyses of six pericentromeric/centromeric-specific repeats demonstrated dynamic fluctuations in their abundance across seven licorice species during evolutionary divergence approximately 11.96 million years ago (MYA). Notably, we discovered that Gly252-associated young LTR/Gypsy elements not only preferentially inserted into the Gly129-associated satellite, which shares high sequence similarity with their terminal regions, but also maintained a synergistic evolutionary pattern following the independent divergence of licorice species. Collectively, our findings elucidate the structure, distribution, and evolutionary diversity of repetitive elements in the licorice genome, offering new insights into the formation and evolution of pericentromeric/centromeric repeats within the genus Glycyrrhiza.