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The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

The Apiaceae genus Daucus consists of approximately 25 species (including carrots) which are characterized by the presence of bracts in pedunculate umbels, dorsally compressed mericarps, hairs on primary ridges, and uniseriately arranged spines on the secondary ridges of the fruit. Taxonomically, Daucus has been considered to be one of the most problematic genera in the Apiaceae due to the highly variable fruit morphology. Despite taxonomic controversy and economic importance of the genus, no rigorously constructed estimate of phylogenetic relationships exists. To examine generic limit and relationships among species of Daucus and its putatively related taxa, phylogenetic analyses of characters derived from nuclear ribosomal DNA ITS sequences were conducted. Two major clades emerged within Daucus, but neither of them have been previously recognized using morphological characters. The phylogeny also provides taxonomic status of recently reported new species of Daucus, D. arcanus and D. conchitae.

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