Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

Springer Science and Business Media LLC - 2006
Robert K. Jansen1, Charalambos Kaittanis2, Christopher Saski3, Seung Bum Lee2, Jeffrey Tomkins3, Andrew J. Alverson1, Henry Daniell2
1Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX, 78712, USA
2Dept. of Molecular Biology & Microbiology, Biomolecular Science, University of Central Florida, Building #20, Orlando, FL, 32816-2364, USA
3Clemson University Genomics Institute, Clemson University, Biosystems Research Complex, 51, New Cherry Street, SC, 29634, USA

Tóm tắt

AbstractBackgroundThe Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome ofVitis viniferaand used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.ResultsTheVitis viniferachloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order ofVitisis identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion ofGossypiumis necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses placeCucumisas sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade.ConclusionPhylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction.

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Tài liệu tham khảo

Soltis DE, Soltis PS, Endress PK, Chase MW: Phylogeny and evolution of Angiosperms. 2005, Sunderland Massachusetts: Sinauer Associates Inc

Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH: The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol Biol Evol. 2004, 21: 1445-1454. 10.1093/molbev/msh147.

Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH: Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol Biol Evol. 2003, 20: 1499-1505. 10.1093/molbev/msg159.

Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH: Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol. 2005, 22: 1813-1822. 10.1093/molbev/msi173.

Leebens-Mack J, Raubeson LA, Cui L, Kuehl J, Fourcade M, Chumley T, Boore JL, Jansen RK, dePamphilis CW: Identifying the basal angiosperms in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol Biol Evol. 2005, 22: 1948-1963. 10.1093/molbev/msi191.

Chang C-C, Lin H-C, Lin I-P, Chow T-Y, Chen H-H, Chen W-H, Cheng C-H, Lin C-Y, Liu S-M, Chang C-C, Chaw S-M: The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol. 2006, 23: 279-291. 10.1093/molbev/msj029.

Soltis DE, Soltis PS: Amborella not a "basal angiosperm"? Not so fast. Amer J Bot. 2004, 91: 997-1001.

Stefanovic S, Rice DW, Palmer JD: Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?. BMC Evol Biol. 2004, 4: 35-10.1186/1471-2148-4-35.

Martin W, Deusch O, Stawski N, Grunheit N, Goremykin V: Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci. 2005, 10: 203-209. 10.1016/j.tplants.2005.03.007.

Soltis DE, Albert VA, Savolainen V, Hilu K, Qiu Y-Q, Chase MW, Farris JS, Stefanović S, Rice DW, Palmer JD, Soltis PS: Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends Plant Sci. 2004, 9: 477-483. 10.1016/j.tplants.2004.08.008.

Lockhart PJ, Penny D: The place of Amborella within the radiation of angiosperms. Trends Plant Sci. 2005, 10: 201-202. 10.1016/j.tplants.2005.03.006.

Ané C, Burleigh JG, McMahon MM, Sanderson MJ: Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol. 2005, 22: 914-924. 10.1093/molbev/msi076.

Savolainen V, Fay MF, Albach DC, Backlund A, van der Bank M, Cameron KM, Johnson SA, Lledó MD, Pintaud J-C, Powell M, Sheahan MC, Soltis DE, Soltis PS, Weston P, Whitton WM, Wurdack KJ, Chase MW: Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bulletin. 2000, 55: 257-309.

Savolainen V, Chase MW, Morton CM, Soltis DE, Bayer C, Fay MF, De Bruijn A, Sullivan S, Qiu Y-L: Phylogenetics of flowering plants based upon a combined analysis of plastid atpB and rbcL gene sequences. Syst Biol. 2000, 49: 306-362. 10.1080/10635159950173861.

Soltis DE, Soltis PS, Chase MW, Mort ME, Albach DC, Zanis M, Savolainen V, Hahn WJ, Hoot SB, Fay MF, Axtell M, Swensen SM, Prince LM, Kress WJ, Nixon KC, Farris JS: Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot J Linn Soc. 2000, 133: 381-461. 10.1006/bojl.2000.0380.

Soltis DE, Senters AE, Zanis MJ, Kim S, Thompson JD, Soltis PS, Ronse De Craene LP, Endress PK, Farris KS: Gunnerales are sister to other core eudicots: implications for the evolution of pentamery. Amer J Bot. 2003, 90: 461-470.

Cronquist A: An integrated system of classification of flowering plants. 1981, Boston Massachusetts: Columbia University Press

Chase M, Soltis D, Olmstead R, Morgan D, Les D, Mishler B, Duvall M, Price R, Hills H, Qui Y-L, Kron K, Rettig J, Conti E, Palmer J, Manhart J, Sytsma K, Michaels H, Kress J, Karol K, Clark D, Hedren M, Gaut B, Jansen R, Kim K-J, Wimpee C, Smith J, Furnier G, Straus S, Xiang Q-Y, Plunkett G, Soltis P, Swensen S, Williams S, Gadek P, Quinn C, Equiarte L, Golenberg E, Learn G, Graham S, Barrett S, Dayanandan S, Albert V: Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbc L. Ann Missouri Bot Gard. 1993, 80: 528-580. 10.2307/2399846.

Hilu KW, Borsch T, Muller K, Soltis DE, Soltis PS, Savolainen V, Chase M, Powell M, Alice L, Evans R, Sauquet H, Neinhuis C, Slotta T, Rohwer J, Chatrou L: Inference of angiosperm phylogeny based on matK sequence information. Amer J Bot. 2003, 90: 1758-1776.

Daniell H, Kumar S, Duformantel N: Breakthrough in chloroplast genetic engineering of agronomically important crops. Trends Biotechnol. 2005, 23: 238-245. 10.1016/j.tibtech.2005.03.008.

The Food and Agriculture Organization of the United Nations: FAO Statitstical Databases – Agricultural Production. [http://faostat.fao.org/]

Foreign Agricultural Services, US Department of Agriculture: World Horticultural Trade and U.S. Export Opportunities. 2005, [http://www.fas.usda.gov/htp/horticulture/Grapes/]

DeCosa B, Moar W, Lee SB, Miller M, Daniell H: Overexpression of the Bt Cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals. Nat Biotechnol. 2001, 9: 71-74.

Ruiz ON, Hussein H, Terry N, Daniell H: Phytoremediation of organomercurial compounds via chloroplast genetic engineering. Plt Phys. 2003, 32: 1344-1352. 10.1104/pp.103.020958.

Lossl A, Eibl C, Harloff HJ, Jung C, Koop HU: Polyester synthesis in transplastomic tobacco (Nicotiana tabacum L.): significant contents of polyhydroxybutyrate are associated with growth reduction. Plant Cell Rep. 2003, 21: 891-899.

Quesada-Vargas T, Ruiz ON, Daniell H: Characterization of heterologous multigene operons in transgenic chloroplasts: transcription, processing, translation. Plt Physiol. 2005, 138: 1746-1762. 10.1104/pp.105.063040.

Daniell H, Datta R, Varma S, Gray S, Lee SB: Containment of herbicide resistance through genetic engineering of the chloroplast genome. Nat Biotechnol. 1998, 16: 345-348. 10.1038/nbt0498-345.

Daniell H: Molecular strategies for gene containment in transgenic crops. Nat Biotechnol. 2002, 20: 581-586. 10.1038/nbt0602-581.

Hagemann R: The Sexual Inheritance of Plant Organelles. Molecular Biology and Biotechnology of Plant Organelles. Edited by: Daniell H, Chase C. 2004, The Netherlands: Springer Publishers, 93-113.

Ruiz ON, Daniell H: Engineering cytoplasmic male sterility via the chloroplast genome. Plt Physiol. 2005, 138: 1232-1246. 10.1104/pp.104.057729.

Lee SB, Kwon HB, Kwon SJ, Park SC, Jeong MJ, Han SE, Daniell H: Accumulation of trehalose within transgenic chloroplasts confers drought tolerance. Mol Breed. 2003, 11: 1-13. 10.1023/A:1022100404542.

Dhingra A, Portis AR, Daniell H: Enhanced translation of a chloroplast expressed rbcS gene restores SSU levels and photosynthesis in nuclear antisense rbcS plants. Proc Natl Acad Sci USA. 2004, 101: 6315-6320. 10.1073/pnas.0400981101.

Daniell H, Lee SB, Panchal T, Wiebe PO: Expression of cholera toxin B subunit gene and assembly as functional oligomers in transgenic tobacco chloroplasts. J Mol Biol. 2001, 311: 1001-1009. 10.1006/jmbi.2001.4921.

Leelavathi S, Gupta N, Maiti S, Ghosh A, Reddy VS: Overproduction of an alkali- and thermo-stable xylanase in tobacco chloroplasts and efficiency recovery of the enzyme. Mol Breed. 2003, 11: 59-67. 10.1023/A:1022168321380.

Grevich JJ, Daniell H: Chloroplast genetic engineering: recent advances and future perspectives. Crit Rev Plt Sci. 2005, 24: 83-108. 10.1080/07352680590935387.

McBride KE, Svab Z, Schaaf DJ, Hogan PS, Stalker DM, Maliga P: Amplification of a chimeric Bacillus gene in chloroplasts leads to an extraordinary level of an insecticidal protein in tobacco. Bio/Technology. 1995, 13: 362-365. 10.1038/nbt0495-362.

Kota M, Daniel H, Varma S, Garczynski SF, Gould F, William MJ: Overexpression of the Bacillus thuringiensis (Bt) Cry2Aa2 protein in chloroplasts confers resistance to plants against susceptible and Bt-resistant insects. Proc Natl Acad Sci USA. 1999, 96: 1840-1845. 10.1073/pnas.96.5.1840.

Iamtham S, Day A: Removal of antibiotic resistance genes from transgenic tobacco plastids. Nat Biotechnol. 2000, 18: 1172-1176. 10.1038/81161.

DeGray G, Rajasekaran K, Smith F, Sanford J, Daniell H: Expression of an antimicrobial peptide via the chloroplast genome to control phytopathogenic bacteria and fungi. Plt Phys. 2001, 127: 852-862. 10.1104/pp.127.3.852.

Kumar S, Dhingra A, Daniell H: Plastid expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots and leaves confers enhanced salt tolerance. Plant Physiol. 2004, 136: 2843-2854. 10.1104/pp.104.045187.

Raubeson LA, Jansen RK: Chloroplast genomes of plants. Diversity and Evolution of Plants-Genotypic and Phenotypic Variation in Higher Plants. Edited by: Henry H. 2005, Wallingford: CABI Publishing, 45-68.

Kato T, Kaneko T, Sato S, Nakamura Y, Tabata S: Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 2000, 7: 323-330. 10.1093/dnares/7.6.323.

Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH: The chloroplast genome of the "basal" angiosperm Calycanthus fertilis – structural and phylogenetic analyses. Plt Syst Evol. 2003, 242: 119-135. 10.1007/s00606-003-0056-4.

Hupfer H, Swaitek M, Hornung S, Herrmann RG, Maier RM, Chiu WL, Sears B: Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome 1 of the five distinguishable Euoenthera plastomes. Mol Gen Genet. 2000, 263: 581-585.

Spielmann A, Roux E, von Allmen J, Stutz E: The soybean chloroplast genome: completed sequence of the rps19 gene, including flanking parts containing exon 2 of rpl2 (upstream), but lacking rpl22 (downstream). Nucl Acids Res. 1988, 16: 1199-

Milligan BG, Hampton JN, Palmer JD: Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol Biol Evol. 1989, 6: 355-368.

Gantt JS, Baldauf SL, Calie PJ, Weeden NF, Palmer JD: Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 1991, 10: 3073-3078.

Doyle JJ, Doyle JL, Palmer JD: Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst Bot. 1995, 20: 272-294.

Saski C, Lee S, Daniell H, Wood T, Tomkins J, Kim H-G, Jansen RK: Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plt Mol Biol. 2005, 59: 309-322. 10.1007/s11103-005-8882-0.

Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermlin LS, Wolfe KH: Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. The Plant Cell. 2001, 13: 645-658. 10.1105/tpc.13.3.645.

Cosner ME, Jansen RK, Palmer JD, Downie SR: The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr Genet. 1997, 31: 419-429. 10.1007/s002940050225.

Downie SR, Palmer JD: Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. Molecular Systematics of Plants. Edited by: Soltis PS, Soltis DE, Doyle JJ. 1992, New York: Chapman and Hall, 14-35.

Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH, Stern DB: The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. The Plt Cell. 2002, 14: 1-22. 10.1105/tpc.140110.

Pombert J-F, Otis C, Lemieux C, Turmel M: The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol. 2005, 22: 1903-1918. 10.1093/molbev/msi182.

Lee S-B, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H: The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics. 2006, 7: 61-10.1186/1471-2164-7-61.

Palmer JD: Plastid chromosomes: structure and evolution. The Molecular Biology of Plastids. Edited by: Bogorad L, Vasil K. 1991, San Diego: Academic Press, 5-53.

Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM: The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol. 2002, 19: 1602-1612.

Hirose T, Kusumegi T, Tsudzuki T, Sugiura M: RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity. Mol Gen Genet. 1999, 262: 462-467. 10.1007/s004380051106.

Wolf PG, Rowe CA, Hasebe M: High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene. 2004, 339: 89-97. 10.1016/j.gene.2004.06.018.

Fiebig A, Stegemann S, Bock R: Rapid evolution of RNA editing sites in a small non-essential plastid gene. Nucl Acids Res. 2004, 32: 3615-3622. 10.1093/nar/gkh695.

Monde RA, Schusterc G, Stern DB: Processing and degradation of chloroplast mRNA. Biochimie. 2000, 82: 573-582. 10.1016/S0300-9084(00)00606-4.

Rochaix JD: Posttranscriptional control of chloroplast gene expression. From RNA to photosynthetic complex. Plt Phys. 2001, 125: 142-144. 10.1104/pp.125.1.142.

Donoghue MJ, Doyle JA: Phylogenetic studies of seed plants and angiosperms based on morphological characters. The Hierarchy of Life: Molecules and Morphology in Phylogenetic Studies. Edited by: Bremer K, Jornvall H. 1989, Amersterdam: Elsevier Science Publishers, 181-193.

Doyle JA, Hotton CL: Diversification of early angiosperm pollen in a cladistic context. Pollen and Spores: Patterns of Diversification. Edited by: Blackmore S, Barnes SH. 1991, Oxford: Clarendon, 169-195.

Soltis DE, Soltis PS, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, Sweere JA, Kuzoff RK, Kron KA, Chase M, Swensen SM, Zimmer E, Shaw SM, Gillespie LJ, Kress WJ, Sytsma K: Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann Missouri Bot Gard. 1997, 84: 1-49. 10.2307/2399952.

Hoot SB, Magallón S, Crane PR: Phylogeny of basal eudicots based on three molecular data sets: atpB, rbcL, and 18S nuclear ribosomal DNA sequences. Ann Missouri Bot Gard. 1999, 86: 1-32. 10.2307/2666215.

Soltis PS, Soltis DE, Chase MW: Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature. 1999, 402: 402-40. 10.1038/46528.

Rokas A, Williams BL, King N, Carrol SB: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003, 425: 798-804. 10.1038/nature02053.

Swofford DL, Olsen GJ, Waddell PJ, Hillis DM: Phylogenetic inference. Molecular Systematics. Edited by: Hillis DM, Moritz C, Mable BK. 1996, Massachusetts: Sinauer Associates Inc, 407-514.

Bruno WJ, Halpern AL: Topological bias and inconsistency of maximum likelihood using wrong models. Mol Biol Evol. 1999, 16: 564-566.

Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS: Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol. 2001, 50: 525-539. 10.1080/106351501750435086.

Huelsenbeck JP, Ronquist F, Nielson R, Bolback JP: Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 2001, 294: 2310-2314. 10.1126/science.1065889.

Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L: Methods for obtaining and analyzing chloroplast genome sequences. Meth Enzym. 2005, 395: 348-384. 10.1016/S0076-6879(05)95020-9.

Clemson University BAC/EST Resource Center: [http://www.genome.clemson.edu]

Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8: 186-194.

Wyman SK, Boore JL, Jansen RK: Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004, 20: 3252-3255. 10.1093/bioinformatics/bth352. [http://bugmaster.jgi-psf.org/dogma]

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R: REPuter: the manifold applications of repeat analysis on a genomic scale. Nucl Acids Res. 2001, 29: 4633-4642. 10.1093/nar/29.22.4633.

Higgins DG, Thompson JD, Gibson TJ: Using CLUSTAL for multiple sequence alignments. Meth Enzy. 1996, 266: 383-402.

Cui L, Veeraraghavan N, Richer A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, de Pamphillis CW: ChloroplastDB: the chloroplast genome database. Nucl Acids Res. 2006, 34: D692-D696. 10.1093/nar/gkj055. [http://chloroplast.cbio.psu.edu/]

Swofford DL: PAUP*: Phylogenetic analysis using parsimony (*and other methods), ver. 4.0. 2003, Sunderland MA: Sinauer Associates

Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14: 817-818. 10.1093/bioinformatics/14.9.817.

Sullivan J, Abdo Z, Joyce P, Swofford DL: Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol Biol Evol. 2005, 22: 1386-1392. 10.1093/molbev/msi129.

Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985, 39: 783-791.

Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M: Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA. 1994, 91: 9794-9798.

Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M: 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. 1989, 217: 185-194.

Asano T, Tsudzuki T, Takahashi S, Shimada H, Kadowaki K: Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res. 2004, 11: 93-99. 10.1093/dnares/11.2.93.

Maier RM, Neckermann K, Igloi GL, Kossel H: Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol. 1995, 251: 614-628. 10.1006/jmbi.1995.0460.

Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S: Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 1999, 6: 283-290. 10.1093/dnares/6.5.283.

Steane DA: Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res. 2005, 12: 215-220.

Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M: The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986, 5: 2043-2049.

Kim K-J, Lee H-L: Complete chloroplast genome sequence from Korean Ginseng (Panax schiseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004, 11: 247-261. 10.1093/dnares/11.4.247.

Daniell H, Lee S-B, Grevich J, Saksi C, Quesada-Vargas T, Guda C, Tomkins J, Jansen RK: Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl. 2006,

Schmitz-Linneweber C, Maier RM, Alcaraz JP, Cottet A, Herrmann RG, Mache R: The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plt Mol Biol. 2001, 45: 307-315. 10.1023/A:1006478403810.

APG II 2002: An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants APG II. Bot J Linn Soc. 2003, 141: 399-436. 10.1046/j.1095-8339.2003.t01-1-00158.x.

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