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Most plants belonging to the widely distributed genus  Dianthus  are used for gardening. Interspecific hybridization of different  Dianthus  species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among  Dianthus  species, the chloroplast genomes of 12  Dianthus  species, including nine  Dianthus gratianopolitanus  varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474–149,735 bp), with  Dianthus caryophyllus  having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of  Dianthus , we identified 124–126 annotated genes, including 83–84 protein-coding genes. Notably,  D. caryophyllus  had 83 protein-coding genes but lacked  rpl2 . The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of  Dianthus  indicated that  D. caryophyllus  and  D. gratianopolitanus  were most closely related, suggesting that the degree of variation within nine  Dianthus  varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within  Dianthus  species.

Distinguish Dianthus species or varieties based on chloroplast genomes