The complete chloroplast genome of Euphorbia fauriei, isolated from Busan, Republic of Korea

The characterization of Euphorbia fauriei chloroplast genome, isolated from Busan, Republic of Korea.</p

Distribution of tetra, penta and hexapolymer single sequence repeats (SSRs) in the <i>Dianthus</i> chloroplast genome.

<p>Distribution of tetra, penta and hexapolymer single sequence repeats (SSRs) in the <i>Dianthus</i> chloroplast genome.</p

Molecular phylogenetic tree analysis of cp protein-coding gene <i>infA</i> of 32 Angiosperms.

<p>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. <i>Nelumbo</i> was set as the outgroup.</p

The K_A/K_S values of 76 genes encoded by 87 protein-coding exons of <i>D</i>. <i>superbus</i> var. <i>longicalycinus</i>, <i>L</i>. <i>chalcedonica</i> and <i>S</i>. <i>oleracea</i>.

<p>Solid black and open boxes indicate the K_A/K_S ratio of the <i>D</i>. <i>superbus</i> var. <i>longicalycinus</i> vs. <i>L</i>. <i>chalcedonica</i> and <i>D</i>. <i>superbus</i> var. <i>longicalycinus</i> vs. <i>S</i>. <i>oleracea</i>.</p

Comparison of the borders of the LSC, SSC and IR regions of <i>D</i>. <i>superbus</i> var. <i>longicalycinus</i>, <i>N</i>. <i>tabacum</i>, <i>L</i>. <i>chalcedonica</i> and <i>S</i>. <i>oleracea</i> cp genomes.

<p>(ψ refers to the pseudogene of <i>rps19</i> at the IRA/LSC border of <i>D</i>. <i>superbus</i> var. <i>longicalycinus</i>). Blue numbers indicate the amount of bp present and red indicates gaps between genes and junctions.</p

Molecular phylogenetic tree analysis of cp protein-coding gene <i>rpl23</i> of 32 Angiosperms.

<p>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. <i>Nelumbo</i> was set as the outgroup.</p

List of identified simple sequence repeats of the <i>Dianthus</i> chloroplast genome.

<p>List of identified simple sequence repeats of the <i>Dianthus</i> chloroplast genome.</p

Molecular phylogenetic tree of 32 Angiosperms based on 78 protein-coding genes in the cp genome.

<p>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. <i>Nelumbo</i> was set as the outgroup.</p

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

<div><p><i>Dianthus superbus</i> var. <i>longicalycinus</i> is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study, <i>D</i>. <i>superbus</i> was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as <i>Lychnis chalcedonica</i> and <i>Spinacia oleracea</i>. <i>D</i>. <i>superbus</i> 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 (<i>rps19</i>) 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 (<i>infA</i>) and ribosomal protein subunit L23 (<i>rpl23</i>) genes were absent from the <i>Dianthus</i> cp genome. When the cp genome of <i>Dianthus</i> was compared with 31 other angiosperm lineages, the <i>infA</i> gene was found to have been lost in most members of rosids, solanales of asterids and <i>Lychnis</i> of Caryophyllales, whereas <i>rpl23</i> gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of <i>Dianthus</i> and <i>Spinacia</i> has two introns in the proteolytic subunit of ATP-dependent protease (<i>clpP</i>) gene, but <i>Lychnis</i> has lost introns from the <i>clpP</i> gene. Furthermore, phylogenetic analysis of individual protein-coding genes <i>infA</i> and <i>rpl23</i> revealed that gene loss or pseudogenization occurred independently in the cp genome of <i>Dianthus</i>. Molecular phylogenetic analysis also demonstrated a sister relationship between <i>Dianthus</i> and <i>Lychnis</i> 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, <i>D</i>. <i>superbus</i> var. <i>longicalycinus</i>.</p></div

List of genes present in the <i>Dianthus</i> chloroplast genome.

<p>^a—Two gene copies in IRs;</p><p>^b—Gene containing a single intron;</p><p>^c—Gene containing two introns;</p><p>^d—Gene divided into two independent transcription units;</p><p>^e—Pseudogene.</p><p>List of genes present in the <i>Dianthus</i> chloroplast genome.</p