Comparative analysis of chloroplast genomes and transcriptomics reveals the adaptation of <i>Glycyrrhiza</i> to salt stress

<i>Glycyrrhiza</i> is a perennial leguminous plant with salt tolerance, and its roots and rhizomes possess extremely significant medicinal value. The proper salinity can facilitate the growth of <i>Glycyrrhiza</i> and increase its content of medicinal ingredients. However, excessive salinity can negatively affect growth and medicinal component contents. The salt tolerance mechanism has not yet been fully elucidated, especially the information of chloroplast genome is in short supply. Present research investigated the genetic diversity of <i>Glycyrrhiza</i> by conducting comparative genomic, adaptive evolutionary, haplotype, population structure, and phylogenetic analyses of the chloroplast genes. Transcriptome analysis revealed that the chloroplast genes of different <i>Glycyrrhiza</i> varieties respond to salt stress at different stages and that these responsive genes are associated predominantly with the photosynthetic structure and regulation of protein synthesis. The editing efficiency of the psbA and rrn23 genes increases significantly under salt stress, potentially contributing to plant adaptation. In summary, analysis of the chloroplast genome provided valuable insights into the genetic diversity and phylogenetic relationships of <i>Glycyrrhiza</i>. Furthermore, transcriptomic data supplemented existing knowledge on chloroplast-mediated salt tolerance mechanisms, offering a foundation for future investigations into the adaptive strategies of <i>Glycyrrhiza</i> under saline conditions.