Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering

Abstract

Datura stramonium is a widely used poisonous plant with great medicinal and economic value. Its chloroplast (cp) genome is 155,871 bp in length with a typical quadripartite structure of the large (LSC, 86,302 bp) and small (SSC, 18,367 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,601 bp). The genome contains 113 unique genes, including 80 protein-coding genes, 29 tRNAs and four rRNAs. A total of 11 forward, 9 palindromic and 13 tandem repeats were detected in the D. stramonium cp genome. Most simple sequence repeats (SSR) are AT-rich and are less abundant in coding regions than in non-coding regions. Both SSRs and GC content were unevenly distributed in the entire cp genome. All preferred synonymous codons were found to use A/T ending codons. The difference in GC contents of entire genomes and of the three-codon positions suggests that the D. stramonium cp genome might possess different genomic organization, in part due to different mutational pressures. The five most divergent coding regions and four non-coding regions (trnH-psbA, rps4-trnS, ndhD-ccsA, and ndhI-ndhG) were identified using whole plastome alignment, which can be used to develop molecular markers for phylogenetics and barcoding studies within the Solanaceae. Phylogenetic analysis based on 68 protein-coding genes supported Datura as a sister to Solanum. This study provides valuable information for phylogenetic and cp genetic engineering studies of this poisonous and medicinal plant.

Figure 1. Gene map of the Datura stramonium chloroplast genome.

Genes drawn inside the circle are transcribed clockwise, and those outside are counterclockwise. Genes belonging to different functional groups are color-coded. The darker gray in the inner circle corresponds to GC content, while the lighter gray corresponds to AT content.

Figure 2. Distribution of SSRs present in the 41 asteridae chloroplast genomes.

Figure 3. Comparison of four chloroplast genomes using mVISTA program.

Grey arrows and thick black lines above the alignment indicate genes with their orientation and the position of the IRs, respectively. A cut-off of 70% identity was used for the plots, and the Y-scale represents the percent identity between 50–100%. Genome regions are color-coded as protein-coding (exon), rRNA, tRNA and conserved noncoding sequences (CNS).

Figure 4. The Ka/Ks ratio of Datura stramonium, Ipomoea purpurea, Nicotiana undulate and Solanum tuberosum for comparison with Nicotiana tabacum.

Figure 5. Comparison of the borders of LSC, SSC and IR regions among six chloroplast genomes.

The IRb/SSC border extended into the ycf1 genes to create various lengths of ycf1 pseudogenes among six chloroplast genomes. The ycf1 pseudogene and the ndhF gene overlapped in the N. tabacum, S. lycopersicum and D. stramonium cp genomes from 3 bp to 20 bp, respectively. Various lengths of rps19 pseudogenes were created at the IRa/LSC borders except N. tabacum. This figure is not to scale.

Figure 6. The ML phylogenetic tree of the asteridae clade based on 68 protein-coding genes.

The ML tree was obtained with the - lnL of 356757.56 using the GTR+I+G nucleotide substitution model. Number above each node are bootstrap support values. Cycas taitungensis was set as outgroup.