Fig 1.
The circos diagram shows the four cp genomes.
The outermost layer and inner layer denotes the % GC content and GC skew in the genome, respectively. The number of each genome indicates the genomic position on the assembly of chloroplast genomes. Similar blocks are connected with lines, and each line represents one unique gene of the genome with the highest similarity between Dianthus and three other cp genomes.
Table 1.
List of genes present in the Dianthus chloroplast genome.
Table 2.
Location and length of intron-containing genes in the Dianthus chloroplast genome.
Fig 2.
Comparison of the cp genome sequence of Dianthus superbus var. longicalycinus, Nicotiana tabacum, Lychnis chalcedonica and Spinacia oleracea generated with mVista.
Gray arrows indicate the position and direction of each gene. Red and blue areas indicate intergenic and genic regions respectively. Black lines define regions of sequence identity with D. superbus var. Longicalycinus, using a 50% identity cutoff. Dashed rectangles denote highly divergent regions of D. superbus var. longicalycinus compared to N. tabacum, L. chalcedonica and S. oleracea.
Fig 3.
Comparison of the borders of the LSC, SSC and IR regions of D. superbus var. longicalycinus, N. tabacum, L. chalcedonica and S. oleracea cp genomes.
(ψ refers to the pseudogene of rps19 at the IRA/LSC border of D. superbus var. longicalycinus). Blue numbers indicate the amount of bp present and red indicates gaps between genes and junctions.
Fig 4.
Molecular phylogenetic tree analysis of cp protein-coding gene infA of 32 Angiosperms.
The tree was constructed by maximum likelihood (ML) analysis using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Nelumbo was set as the outgroup.
Fig 5.
Molecular phylogenetic tree analysis of cp protein-coding gene rpl23 of 32 Angiosperms.
The tree was constructed by maximum likelihood (ML) analysis using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Nelumbo was set as the outgroup.
Table 3.
List of identified simple sequence repeats of the Dianthus chloroplast genome.
Table 4.
Distribution of tetra, penta and hexapolymer single sequence repeats (SSRs) in the Dianthus chloroplast genome.
Table 5.
Distribution of tandem repeats in the Dianthus chloroplast genome.
Fig 6.
The KA/KS values of 76 genes encoded by 87 protein-coding exons of D. superbus var. longicalycinus, L. chalcedonica and S. oleracea.
Solid black and open boxes indicate the KA/KS ratio of the D. superbus var. longicalycinus vs. L. chalcedonica and D. superbus var. longicalycinus vs. S. oleracea.
Fig 7.
Molecular phylogenetic tree of 32 Angiosperms based on 78 protein-coding genes in the cp genome.
The tree was constructed by maximum likelihood (ML) analysis of the conserved regions using the RaxML program and the GTR+I nucleotide model. The stability of each tree node was tested by bootstrap analysis with 1000 replicates. Bootstrap values are indicated on the branches, and the branch length reflects the estimated number of substitutions per 1000 sites. Nelumbo was set as the outgroup.