Abstract
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.
Highlights
Chloroplasts are double membrane bound plant organelles that encode genes essential for photosynthesis and other biochemical pathways such as biosynthesis of starch, fatty acids, pigments and amino acids [1]
Several unique features were observed in the cp genome of Dianthus, including pseudogenization or gene loss of rps19, initiation factor (infA) and rpl23 genes
When compared with the other 31 angiosperm lineages, the infA gene has been lost from most members of the rosids, solanales of asterids and Lychnis of Caryophyllales, whereas the rpl23 gene was lost or pseudogization has occurred exclusively in the family of Caryophyllales cp genomes
Summary
Chloroplasts are double membrane bound plant organelles that encode genes essential for photosynthesis and other biochemical pathways such as biosynthesis of starch, fatty acids, pigments and amino acids [1] This organelle possesses its own single circular DNA, chromosome, which is highly conserved among species. With the availability of more chloroplast genomes in the database, comparative genome studies have been carried out These investigations have revealed many structural gene rearrangements, large IR expression and the occurrence of gene loss in numerous angiosperm lineages [4,5]. Such studies are essential to reconstruction of plant phylogenetic trees [6], DNA barcoding [7], and population [8] and transplastomic studies [9]
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