Comparative and phylogenetic analyses based on the complete chloroplast genomes of Limonium (Plumbaginaceae) species

Limonium Mill., a genus belonging to the family Plumbaginaceae, is mainly distributed along the Mediterranean coast of Eurasia. It is known for its rich species diversity and remarkable morphological variation, encompassing both herbaceous and semi-shrub forms. Some species of Limonium have medicinal, economic, and ornamental value in China. However, their genomic and phylogenetic relationships remain unclear. In this study, we sequenced and assembled complete chloroplast genomes of eight Limonium species to address this issue. We conducted comparative and phylogenetic analyses to investigate the genetic structural characteristics and clarify the taxonomic status of 12 Limonium species.

The newly obtained circular chloroplast genomes of the eight Limonium species had a quadripartite structure and ranged from 154,545 to 154,960 bp in length. All species contained 128 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Despite minor variations in the inverted repeat (IR) boundary regions, the overall genome structure and gene content remained relatively conserved. The rpl16 gene lost its intron and the rpl23gene underwent pseudogenization. We identified 55-73 SSRs repeat sequences and three nucleotide diversity regions that will be used for population genetics and molecular phylogenetic studies of the Limonium genus. The robust phylogenetic tree suggests that species belonging to these sections in Xinjiang, China, have accumulated substantial genetic divergence over long-term evolution, resulting in stable phylogenetic relationships.

The complete chloroplast genomes of Limonium increase our understanding of the genetic diversity and evolution of Limonium species and further aid in the exploration and utilization of Limonium plants.