Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Liu, Yue ^a,b,c,d   Huo, Naxin ^c   Dong, Lingli ^c   Wang, Yi ^c   Zhang, Shuixian ^a   Young, Hugh A ^c   Feng, Xiaoxiao ^a   Gu, Yong Qiang ^c  

^a MINZU UNIVERSITY OF CHINA   (China)

^b INSTITUTE OF CHINESE MATERIA MEDICA   (China)

^c WESTERN REGIONAL RESEARCH CENTER   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGERATINA ADENOPHORA; ARTEMISIA FRIGIDA; ARTICLE; ASTERACEAE; CHLOROPLAST GENOME; CONTROLLED STUDY; DNA SEQUENCE; GENE DUPLICATION; GENE LOCUS; GENETIC ANALYSIS; GUIZOTIA ABYSSINICA; HELIANTHUS ANNUUS; INVERTED REPEAT; LARGE SINGLE COPY; LETTUCE; MEDICINAL PLANT; MONGOLIAN MEDICINE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; POPULATION GENETICS; PYROSEQUENCING; SMALL SINGLE COPY; ARTEMISIA; CHROMOSOME INVERSION; GENE DOSAGE; GENETICS; MOLECULAR GENETICS; MONGOLIA; NUCLEOTIDE REPEAT; REPRODUCIBILITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ARTEMISIA; ASTERACEAE; BASE SEQUENCE; CHROMOSOME INVERSION; GENE DOSAGE; GENES, PLANT; GENOME, CHLOROPLAST; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; MONGOLIA; PHYLOGENY; PLANTS, MEDICINAL; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84874534534     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057533     Document Type: Article

References (85)

1. Liu Y, Liu J, Tang L, Zhang W, Zhang L, et al. (2008) Current Status Research of Mongolian Medicine Artemisia Frigida Willd. Studies of Trace Elements and Health 25: 55-57.
2. Bremer K (1994) Asteraceae- Cladistics and Classification. Portland, Oregon, USA: Timber Press.
3. Garcia S, Sanz M, Garnatje T, Kreitschitz A, McArthur ED, et al. (2004) Variation of DNA amount in 47 populations of the subtribe Artemisiinae and related taxa (Asteraceae, Anthemideae): karyological, ecological, and systematic implications. Genome 47: 1004-1014.
4. Wan T, Sun Q, Cai P, Meng X, Yi W, et al. (2011) Observation of chromosome karyotypes of Artemisia frigida in different ecological areas of Inner Mongolia. Acta Botanica Boreali-Occidentalia Sinica 31: 456-461.
5. Tian YH (2000) Chinese national medicine processing integration. Beijing: Chines Ancient Books Press.
6. Zhang W, Tang L, Xie K, Cui J, (2008) Determination of total flavonoids in raw and charred Mongolian drug Agi. Li Shizhen Medicine and Materia Medica Research 19: 2952-2953.
7. Cui J, Tang L, Lan R, (2006) Baoyindalai (2006) Clinical analysis of 63 cases on curative effect of Arteisia frigida Wild in treatment of hemoptysis caused by bronchiectasis. Journal of Minzu University of China (natural sciences edition) 15: 149-155.
8. Piao XL, Xie K, Cui J, (2009) Fatty components of Artemisia frigida before and after carbonization by GC-MS. Li Shizhen Medicine and Materia Medica Research 20: 1848-1849.
9. Wang QH, Ao WL, Wang XL, Bao XH, Wang JH, (2010) Two new flavonoid glycosides from Artemisia frigida Willd. J Asian Nat Prod Res 12: 950-954.
10. Taberlet P, Gielly L, Pautou G, Bouvet J, (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
11. Tkach NV, Hoffmann MH, Roser M, Korobkov AA, von Hagen KB, (2008) Parallel evolutionary patterns in multiple lineages of arctic Artemisia L. (Asteraceae). Evolution 62: 184-198.
12. Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, et al. (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zool 6: 16.
13. Garcia S, McArthur ED, Pellicer J, Sanderson SC, Valles J, et al. (2011) A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): Untangling the sagebrushes. Am J Bot 98: 638-653.
14. Hiiesalu I, Opik M, Metsis M, Lilje L, Davison J, et al. (2012) Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing. Mol Ecol 21: 2004-2016.
15. Frank DA, Pontes AW, Maine EM, Caruana J, Raina R, et al. (2010) Grassland root communities: species distributions and how they are linked to aboveground abundance. Ecology 91: 3201-3209.
16. Riggins CW, Seigler DS, (2012) The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: Molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective. Mol Phylogenet Evol 64: 471-490.
17. Palmer JD (1991) Plastid chromosomes: structure and evolution; Bogorad L, Vasil IK, editors. San Diego: Academic Press.
18. Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, et al. (2006) The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol 23: 2175-2190.
19. Jansen RK, Palmer JD, (1987) A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc Natl Acad Sci U S A 84: 5818-5822.
20. Doyle JJ, Doyle JL, Ballenger JA, Palmer JD, (1996) The distribution and phylogenetic significance of a 50-kb chloroplast DNA inversion in the flowering plant family Leguminosae. Mol Phylogenet Evol 5: 429-438.
21. Doyle JJ, Davis JI, Soreng RJ, Garvin D, Anderson MJ, (1992) Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proc Natl Acad Sci U S A 89: 7722-7726.
22. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, et al. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5: 2043-2049.
23. De Cosa B, Moar W, Lee SB, Miller M, Daniell H, (2001) Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals. Nat Biotechnol 19: 71-74.
24. Ruiz ON, Hussein HS, Terry N, Daniell H, (2003) Phytoremediation of organomercurial compounds via chloroplast genetic engineering. Plant Physiol 132: 1344-1352.
25. Quesada-Vargas T, Ruiz ON, Daniell H, (2005) Characterization of heterologous multigene operons in transgenic chloroplasts: transcription, processing, and translation. Plant Physiol 138: 1746-1762.
26. Hagemann R (2004) The sexual inheritance of plant organelles; Daniell H, Chase CD, editors: Springer, Dordrecht, The Netherlands.
27. Dufourmantel N, Pelissier B, Garcon F, Peltier G, Ferullo JM, et al. (2004) Generation of fertile transplastomic soybean. Plant Mol Biol 55: 479-489.
28. Kumar S, Dhingra A, Daniell H, (2004) Plastid-expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots, and leaves confers enhanced salt tolerance. Plant Physiol 136: 2843-2854.
29. Kumar S, Dhingra A, Daniell H, (2004) Stable transformation of the cotton plastid genome and maternal inheritance of transgenes. Plant Mol Biol 56: 203-216.
30. Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, et al. (2010) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res 17: 11-22.
31. Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, et al. (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol 6: 17.
32. Yang M, Zhang X, Liu G, Yin Y, Chen K, et al. (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5: e12762.
33. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, et al. (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36: e122.
34. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
35. Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
36. Wyman SK, Jansen RK, Boore JL, (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255.
37. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
38. Timme RE, Kuehl JV, Boore JL, Jansen RK, (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94: 302-312.
39. Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, et al. (2010) Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour 10: 1048-1058.
40. Kumar S, Hahn FM, McMahan CM, Cornish K, Whalen MC, (2009) Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines. BMC Plant Biol 9: 131.
41. Nie X, Lv S, Zhang Y, Du X, Wang L, et al. (2012) Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS One 7: e36869.
42. Doorduin L, Gravendeel B, Lammers Y, Ariyurek Y, Chin AWT, et al. (2011) The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res 18: 93-105.
43. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I, (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32: W273-279.
44. Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 6: 77.
45. Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, et al. (2007) Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol 45: 547-563.
46. Kurtz S, Schleiermacher C, (1999) REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427.
47. Thiel T, Michalek W, Varshney RK, Graner A, (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.
48. Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, et al. (2007) Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet 115: 571-590.
49. Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH, (2003) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm. Mol Biol Evol 20: 1499-1505.
50. Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, et al. (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6: 32.
51. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
52. Young HA, Lanzatella CL, Sarath G, Tobias CM, (2011) Chloroplast genome variation in upland and lowland switchgrass. PLoS One 6: e23980.
53. Panero JL, Funk VA, (2008) The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed. Mol Phylogenet Evol 47: 757-782.
54. Edgar RC, (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
55. Wang W, Messing J, (2011) High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS One 6: e24670.
56. Nock CJ, Waters DL, Edwards MA, Bowen SG, Rice N, et al. (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol J 9: 328-333.
57. Zhang T, Zhang X, Hu S, Yu J, (2011) An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform. Plant Methods 7: 38.
58. Neckermann K, Zeltz P, Igloi GL, Kossel H, Maier RM, (1994) The role of RNA editing in conservation of start codons in chloroplast genomes. Gene 146: 177-182.
59. Kim KJ, Jansen RK, (1995) ndhF sequence evolution and the major clades in the sunflower family. Proc Natl Acad Sci U S A 92: 10379-10383.
60. Kim KJ, Choi KS, Jansen RK, (2005) Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Mol Biol Evol 22: 1783-1792.
61. Raubeson LA, Jansen RK, (1992) Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255: 1697-1699.
62. Tangphatsornruang S, Uthaipaisanwong P, Sangsrakru D, Chanprasert J, Yoocha T, et al. (2011) Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene 475: 104-112.
63. Palmer JD, Nugent JM, Herbon LA, (1987) Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proc Natl Acad Sci U S A 84: 769-773.
64. Ogihara Y, Terachi T, Sasakuma T, (1988) Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci U S A 85: 8573-8577.
65. Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, et al. (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217: 185-194.
66. Provan J, Powell W, Hollingsworth PM, (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16: 142-147.
67. Jakobsson M, Sall T, Lind-Hallden C, Hallden C, (2007) Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. Theor Appl Genet 114: 223-235.
68. Ebert D, Peakall R, (2009) Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour 9: 673-690.
69. Provan J, Corbett G, Waugh R, McNicol JW, Morgante M, et al. (1996) DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats. Proc Biol Sci 263: 1275-1281.
70. Provan J, Russell JR, Booth A, Powell W, (1999) Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum. Mol Ecol 8: 505-511.
71. Provan J, Corbett G, McNicol JW, Powell W, (1997) Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome 40: 104-110.
72. Bryan GJ, McNicol JW, Meyer RC, Ramsay G, De Jong WS, (1999) Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants. Theoretical and Applied Genetics 99: 859-867.
73. Flannery ML, Mitchell FJ, Coyne S, Kavanagh TA, Burke JI, et al. (2006) Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs. Theor Appl Genet 113: 1221-1231.
74. Provan J, (2000) Novel chloroplast microsatellites reveal cytoplasmic variation in Arabidopsis thaliana. Mol Ecol 9: 2183-2185.
75. Denda T, Watanabe K, Kosuge K, Yahara T, Ito M, (1999) Molecular phylogeny of Brachycome (Asteraceae) Plant Systematics And Evolution. 217: 299-311.
76. Fernandez IA, Aguilar JF, Panero JL, Feliner GN, (2001) A phylogenetic analysis of Doronicum (Asteraceae, Senecioneae) based on morphological, nuclear ribosomal (ITS), and chloroplast (trnL-F) evidence. Mol Phylogenet Evol 20: 41-64.
77. Terry R, Brown G, Olmstead R, (1997) Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF. Am J Bot 84: 664.
78. Scotland RW, Sweere JA, Reeves PA, Olmstead RG, (1995) Higher-level systematics of Acanthaceae determined by Chloroplast DNA sequences American Journal of Botany. 82: 266-275.
79. Catalan P, Kellogg EA, Olmstead RG, (1997) Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences. Mol Phylogenet Evol 8: 150-166.
80. Palmer JD, Jansen RK, Michaels HJ, Chase MW, Manhart JR, (1988) Chloroplast DNA Variation and Plant Phylogeny. Annals of the Missouri Botanical Garden 75: 1180-1206.
81. Kajita T, Kamiya K, Nakamura K, Tachida H, Wickneswari R, et al. (1998) Molecular phylogeny of Dipetrocarpaceae in Southeast Asia based on nucleotide sequences of matK, trnL intron, and trnL-trnF intergenic spacer region in chloroplast DNA. Mol Phylogenet Evol 10: 202-209.
82. Lee JH, Lee JW, Sung JS, Bang KH, Moon SG, (2009) Molecular authentication of 21 Korean artemisia species (Compositae) by polymerase chain reaction-restriction fragment length polymorphism based on trnL-F region of chloroplast DNA. Biol Pharm Bull 32: 1912-1916.
83. Tamura K, Nei M, (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.
84. Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, et al. (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112: 1503-1518.
85. Schulze-Menz GK (1964) A. Engler's: Syllabus der Pflanzenfamilien. Berlin: Gebrüder Borntraeger.