title: 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.
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
authors.forename: Yuanye
authors.initials: Y
authors.lastname: Dang
authors.forename: Dang
authors.initials: D
authors.lastname: Yuanye
authors.affiliation: Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.forename: Li
authors.initials: L
authors.lastname: Qing
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
authors.forename: Jinjian
authors.initials: J
authors.lastname: Lu
authors.forename: Lu
authors.initials: L
authors.lastname: Jinjian
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
authors.forename: Xiwen
authors.initials: X
authors.lastname: Li
authors.forename: Li
authors.initials: L
authors.lastname: Xiwen
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
authors.forename: Yitao
authors.initials: Y
authors.lastname: Wang
authors.forename: Wang
authors.initials: W
authors.lastname: Yitao
mesh_terms: D001482:Base Composition; D003062:Codon; D019295:Computational Biology; D013286:Datura stramonium / Q000145:classification / Q000235:genetics*; D005818:Genetic Engineering; D054628:Genome, Chloroplast; D023281:Genomics; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010946:Plants, Medicinal / Q000145:classification / Q000235:genetics*; D010947:Plants, Toxic / Q000145:classification / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA
chemical_list: D003062:Codon