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.

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

“…Another explanation for the conservation of IR is the presence of conserved rRNA genes in the IR region. The coding regions showing high degree of variation are accD, cemA, petA, psbT , and clpP as also reported for other cp genomes (Yang et al, 2014; Yao et al, 2015). The intergenic region between trnC-GCA–psbD, petD-rps3, psbK-accD, petA-psbT trnK-UUU- rbcL , and ndhJ–ycf3 show high sequence divergence among the legumes aligned.…”

“…The biasness for A and T nucleotide at third codon position is also shown by RSCU analysis for instance, for valine the codon ending with A and T are 36.5% whereas those ending with G and C are 14.75 and 12.25% respectively. Such biasness for high representation of A and T at third codon position is also observed in other land plant plastid genomes (Yang et al, 2014; Yao et al, 2015). It may be due to the compositional bias toward AT rich content (Morton, 2003; Williams et al, 2015).…”

Complete Chloroplast Genome of Castanopsis sclerophylla (Lindl.) Schott: Genome Structures, Comparative and Phylogenetic Analysis

“…The expansion and contraction of IR regions at the borders are the major reason for chloroplast genome size variations and play vital roles in evolution [37–39]. A detailed comparison of four junctions (JLA, JSB, JSA, and JLA) between the two single-copy regions (LSC and SSC) and the two IRs (IRa and IRb) was performed among C. sclerophylla, C. hainanensis, C. echinocarpa and C. concinna by analyzing the exact IR border positions and adjacent genes (Fig.3).…”

The complete chloroplast genome of Chinese medicine (Psoralea corylifolia Linn): Molecular Structures, barcoding analysis, and phylogenetic Analysis

“…We detected a total of 98 SSRs in P. corylifolia including 63 repeats for mononucleotide, 22 repeats for dinucleotide, 2 repeats for trinucleotide, 11 repeats for tetranucleotide, respectively. Because almost all chloroplast genomes had high AT content[47], and almost all SSR loci contained A or T, especially in the mononucleotide (Fig 5). In addition to the SSRs, we identified four type repeats in P. corylifolia , including forward, reverse, complement and palindromic repeats by REPuter.…”