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Dianthus superbus  var.  longicalycinus  is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study,  D .  superbus  was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as  Lychnis chalcedonica  and  Spinacia oleracea .  D .  superbus  had the longest large single copy (LSC) region (82,805 bp), with some variations in the inverted repeat region A (IRA)/LSC regions. The IRs underwent both expansion and constriction during evolution of the Caryophyllaceae family; however, intense variations were not identified. The pseudogene ribosomal protein subunit S19 ( rps19 ) was identified at the IRA/LSC junction, but was not present in the cp genome of other Caryophyllaceae family members. The translation initiation factor IF-1 ( infA ) and ribosomal protein subunit L23 ( rpl23 ) genes were absent from the  Dianthus  cp genome. When the cp genome of  Dianthus  was compared with 31 other angiosperm lineages, the  infA  gene was found to have been lost in most members of rosids, solanales of asterids and  Lychnis  of Caryophyllales, whereas  rpl23  gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of  Dianthus  and  Spinacia  has two introns in the proteolytic subunit of ATP-dependent protease ( clpP ) gene, but  Lychnis  has lost introns from the  clpP  gene. Furthermore, phylogenetic analysis of individual protein-coding genes  infA  and  rpl23  revealed that gene loss or pseudogenization occurred independently in the cp genome of  Dianthus . Molecular phylogenetic analysis also demonstrated a sister relationship between  Dianthus  and  Lychnis  based on 78 protein-coding sequences. The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant,  D .  superbus  var.  longicalycinus .

Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective