Comparative Chloroplast Genomes of Camellia Species

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Yang, Jun Bo ^a   Yang, Shi Xiong ^a   Li, Hong Tao ^a   Yang, Jing ^a   Li, De Zhu ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHLOROPLAST GENOME; CONTROLLED STUDY; GENE DUPLICATION; GENETIC CONSERVATION; GENETIC DIFFERENCE; GENETIC VARIABILITY; INVERTED REPEAT; MOLECULAR SIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TEA;

CAMELLIA; CHLOROPLASTS; COMPUTATIONAL BIOLOGY; GENE ORDER; GENETIC VARIATION; GENOME, CHLOROPLAST; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 84882999542     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073053     Document Type: Article

References (103)

1. Ming TL, Zhang WJ, (1996) The evolution and distribution of genus Camellia. Acta Bot Yunnan 18: 1-13.
2. Kole C, (2011) Wild crop relatives: Genomic and breeding resources cereals. New York: Springer Verlag. p. xxiii, 497.
3. Ming TL, (2000) Monograph of the genus Camellia. Kunming, China: Yunnan Science and Technology Press.
4. Lu HF, Pi EX, Peng QF, Wang LL, Zhang CJ, (2009) A particle swarm optimization-aided fuzzy cloud classifier applied for plant numerical taxonomy based on attribute similarity. Expert Syst Appl 36: 9388-9397. doi:10.1016/j.eswa.2008.12.065.
5. Ming TL, (1999) A systematic synopsis of the genus Camellia. Acta Bot Yunnan 21: 149-159.
6. Ming TL, Bartholomew B, (2007) Theaceae. In: Wu ZY, Raven PH, Hong DY, eds. Flora of China. Beijing & St. Louis: Science Press & Missouri Botanical Garden Press. pp. pp. 367.
7. Vijayan K, Zhang WJ, Tsou CH, (2009) Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences. Am J Bot 96: 1348-1360. doi:10.3732/ajb.0800205. PubMed: 21628283.
8. Vijayan K, Chung MC, Tsou CH, (2012) Dispersion of rDNA loci and its implications on intragenomic variability and phylogenetic studies in Camellia. Sci Hort 137: 59-68. doi:10.1016/j.scienta.2012.01.021.
9. Chang HT, (1998) Flora of Reipublicae Popularis Sinicae. Delectis Florae Republicae Popularis Sinicae, Agendae Academiae Sinicae Edita, Tomus. Beijing, China: Science Press. pp. pp. 101-113.
10. Chang HT, (1981) A taxonomy of the genus Camellia. J Sun Yatsen Univ 1: 1-180.
11. Ye CX, (1997) Classification in the genus Camellia L. American Camellia Society: American Camellia Yeabook. pp. 9-23.
12. Khan N, Mukhtar H, (2007) Tea polyphenols for health promotion. Life Sci 81: 519-533. doi:10.1016/j.lfs.2007.06.011. PubMed: 17655876.
13. Chen L, Zhou ZX, Yang YJ, (2007) Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding. Euphytica 154: 239-248. doi:10.1007/s10681-006-9292-3.
14. Gao JY, Parks CR, Du YQ, (2005) Collected species of the genus Camellia: an illustrated outline. Zhejiang, China: Zhejiang Science and Technology Press.
15. Zhang DL, Yu JF, Chen YZ, Zhang R, (2007) Ornamental teaoil from Camellia cultivars and their hypocotyl graft propagation. SNA Research Conference 52: 257-260.
16. Sealy JR, (1958) A revision of the genus Camellia. Royal Horticultural Society.
17. Chang HT, Bartholomew B, (1984) Camellias. Portland, Oregon, U S A: Timber Press.
18. Thakor BH, Parks CR, (1997) Phylogenetic relationships within the genus Camellia (Theaceae). Am J Bot 84: 237.
19. Thakor BH, (1998) Phylogenetic relationships among the species of genus Camellia (Theaceae). University of North Carolina at Chapel Hill.
20. Tang S, Zhong Y, (2002) A phylogenetic analysis of nrDNA ITS sequences from ser. Chrysantha (Sect. Chrysantha, Camellia, Theaceae). J Genet Mol Biol 13: 105-107.
21. Yang JB, Li HT, Yang SX, Li DZ, Yang YY, (2006) The application of four DNA sequences to studying molecular phylogeny of Camellia (Theaceae). Acta Bot Yunnan 28: 108-114.
22. Xiao T, (2001) Phylogenetic relationships of the genus Camellia (Theaceae) based on the RNA polymerase II (RPB2) sequences. University of North Carolina at Chapel Hill.
23. Xiao TJ, Parks CR, (2002) Molecular analysis of genus Camellia. American Camellia Society: American Camellia Yeabook: pp. 52-58.
24. Fang W, Yang JB, Yang SX, Li DZ, (2010) Phylogeny of Camellia sects. Longipedicellata, Chrysantha and Longissima (Theaceae) based on sequence data of four chloroplast DNA loci. Acta Bot Yunnan 32: 1-13.
25. Su MH, Hsieh CF, Tsou CH, (2009) The confirmation of Camellia formosensis (Theaceae) as an independent species based on DNA sequence analyses. Bot Stud 50: 477-485.
26. Prince LM, Parks CR, (2001) Phylogenetic relationships of Theaceae inferred from chloroplast DNA sequence data. Am J Bot 88: 2309-2320. doi:10.2307/3558391. PubMed: 21669662.
27. Liu Y, Yang SX, Ji PZ, Gao LZ, (2012) Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation. BMC Evol Biol 12: 92. doi:10.1186/1471-2148-12-92. PubMed: 22716114.
28. Pi EX, Peng QF, Lu HF, Shen JB, Du YQ, et al. (2009) Leaf morphology and anatomy of Camellia section Camellia (Theaceae). Bot J Linn Soc 159: 456-476. doi:10.1111/j.1095-8339.2009.00952.x.
29. Lu HF, Shen JB, Lin XY, Fu JL, (2008) Relevance of Fourier transform infrared spectroscopy and leaf anatomy for species classification in Camellia (Theaceae). Taxon 57: 1274-1288.
30. Luna I, Ochoterena H, (2004) Phylogenetic relationships of the genera of Theaceae based on morphology. Cladistics 20: 223-270. doi:10.1111/j.1096-0031.2004.00024.x.
31. Lu HF, Jiang W, Ghiassi M, Lee S, Nitin M, (2012) Classification of Camellia (Theaceae) species using leaf architecture variations and pattern recognition techniques. PLOS ONE 7(1):: e29704. doi:10.1371/journal.pone.0029704. PubMed: 22235330.
32. Jiang B, Peng QF, Shen ZG, Moller M, Pi EX, et al. (2010) Taxonomic treatments of Camellia (Theaceae) species with secretory structures based on integrated leaf characters. Plant Syst Evol 290: 1-20. doi:10.1007/s00606-010-0342-x.
33. Hudson ME, (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 8: 3-17. doi:10.1111/j.1471-8286.2007.02019.x. PubMed: 21585713.
34. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141. doi:10.1016/j.tig.2007.12.007. PubMed: 18262675.
35. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145. doi:10.1038/nbt1486. PubMed: 18846087.
36. 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. doi:10.1093/dnares/dsp025. PubMed: 20007682.
37. 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-. PubMed: 18753151.
38. 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. doi:10.1186/1471-2229-6-17. PubMed: 16934154.
39. Eisen JA, Fraser CM, (2003) Phylogenomics: intersection of evolution and genomics. Science 300: 1706-1707. doi:10.1126/science.1086292. PubMed: 12805538.
40. Delsuc F, Brinkmann H, Philippe H, (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375. doi:10.1038/nrg1603. PubMed: 15861208.
41. Parks M, Cronn R, Liston A, (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7: 84. doi:10.1186/1741-7007-7-84. PubMed: 19954512.
42. Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, et al. (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol 395: 348-384. doi:10.1016/S0076-6879(05)95020-9. PubMed: 15865976.
43. Palmer JD, Stein DB, (1986) Conservation of chloroplast genome structure among vascular plants. Curr Genet 10: 823-833. doi:10.1007/BF00418529.
44. Palmer JD, Jansen RK, Michaels HJ, Chase MW, Manhart JR, (1988) Chloroplast DNA variation and plant phylogeny. Ann Mo Bot Gard 75: 1180-1206. doi:10.2307/2399279.
45. Tian X, Li DZ, (2002) Application of DNA sequences in plant phylogenetic study. Acta Bot Yunnan 24: 170-184.
46. Moore MJ, Bell CD, Soltis PS, Soltis DE, (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci U S A 104: 19363-19368. doi:10.1073/pnas.0708072104. PubMed: 18048334.
47. Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A 104: 19369-19374. doi:10.1073/pnas.0709121104. PubMed: 18048330.
48. Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE, (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci U S A 107: 4623-4628. doi:10.1073/pnas.0907801107. PubMed: 20176954.
49. Zhang YJ, Ma PF, Li DZ, (2011) High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLOS ONE 6: e20596. doi:10.1371/journal.pone.0020596. PubMed: 21655229.
50. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272. doi:10.1101/gr.097261.109. PubMed: 20019144.
51. Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, et al. (2002) 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 19: 1602-1612. doi:10.1093/oxfordjournals.molbev.a004222. PubMed: 12200487.
52. Yukawa M, Tsudzuki T, Sugiura M, (2006) The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Mol Genet Genomics 275: 367-373. doi:10.1007/s00438-005-0092-6. PubMed: 16435119.
53. Kim KJ, Lee HL, (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11: 247-261. doi:10.1093/dnares/11.4.247. PubMed: 15500250.
54. Yi DK, Lee HL, Sun BY, Chung MY, Kim KJ, (2012) The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids. Mol Cells 33: 497-508. doi:10.1007/s10059-012-2281-6. PubMed: 22555800.
55. Meintjes P, Duran C, Kearse M, Moir R, Wilson A, et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):: 1647-1649. doi:10.1093/bioinformatics/bts199. PubMed: 22543367.
56. Wyman SK, Jansen RK, Boore JL, (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. doi:10.1093/bioinformatics/bth352. PubMed: 15180927.
57. Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. doi:10.1093/nar/25.5.955. PubMed: 9023104.
58. Lohse M, Drechsel O, Bock R, (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52: 267-274. doi:10.1007/s00294-007-0161-y. PubMed: 17957369.
59. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29: 4633-4642. doi:10.1093/nar/29.22.4633. PubMed: 11713313.
60. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797. doi:10.1093/nar/gkh340. PubMed: 15034147.
61. Swofford DL, (2002) PAUP*. Phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
62. Wilgenbusch JC, Swofford D, (2003) Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics Chapter 6: Unit 6.4. John Wiley & Sons, Inc., Malden, MA, United States. PubMed: 18428704.
63. Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518. doi:10.1093/nar/gki198. PubMed: 15661851.
64. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818. doi:10.1093/bioinformatics/14.9.817. PubMed: 9918953.
65. Posada D, (2003) Using MODELTEST and PAUP* to select a model of nucleotide substitution. Curr Protoc Bioinformatics Chapter 6: Unit 6.5. John Wiley & Sons, Inc., Malden, MA, United States. PubMed: 18428705.
66. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574. doi:10.1093/bioinformatics/btg180. PubMed: 12912839.
67. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, et al. (2012) MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61: 539-542. doi:10.1093/sysbio/sys029. PubMed: 22357727.
68. 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. doi:10.1371/journal.pone.0012762. PubMed: 20856810.
69. Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202. doi:10.1101/gr.8.3.195. PubMed: 9521923.
70. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error Probabilities Genome Res 8: 186-194.
71. Sugita M, Sugiura M, (1996) Regulation of gene expression in chloroplasts of higher plants. Plant Mol Biol 32: 315-326. doi:10.1007/BF00039388. PubMed: 8980485.
72. Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, et al. (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8: 174. doi:10.1186/1471-2164-8-174. PubMed: 17573971.
73. Gao L, Yi X, Yang YX, Su YJ, Wang T, (2009) Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol 9: 130. doi:10.1186/1471-2148-9-130. PubMed: 19519899.
74. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, et al. (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047. doi:10.1093/bioinformatics/16.11.1046. PubMed: 11159318.
75. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352. PubMed: 19505943.
76. 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. doi:10.3732/ajb.94.3.302. PubMed: 21636403.
77. 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. doi:10.1073/pnas.89.16.7722. PubMed: 1502190.
78. Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH, (2005) Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol 22: 1813-1822. doi:10.1093/molbev/msi173. PubMed: 15930156.
79. Maier RM, Neckermann K, Igloi GL, Kössel H, (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251: 614-628. doi:10.1006/jmbi.1995.0460. PubMed: 7666415.
80. Wu FH, Chan MT, Liao DC, Hsu CT, Lee YW, et al. (2010) Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol 10: 68. doi:10.1186/1471-2229-10-68. PubMed: 20398375.
81. Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, et al. (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol 23: 279-291. PubMed: 16207935.
82. Mardanov AV, Ravin NV, Kuznetsov BB, Samigullin TH, Antonov AS, et al. (2008) Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms. J Mol Evol 66: 555-564. doi:10.1007/s00239-008-9091-7. PubMed: 18463914.
83. 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. doi:10.1016/j.ympev.2007.06.004. PubMed: 17644003.
84. Guisinger MM, Kuehl JV, Boore JL, Jansen RK, (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol 28: 583-600. doi:10.1093/molbev/msq229. PubMed: 20805190.
85. Blazier J, Guisinger MM, Jansen RK, (2011) Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Mol Biol 76: 263-272. doi:10.1007/s11103-011-9753-5. PubMed: 21327834.
86. Palmer JD, Osorio B, Aldrich J, Thompson WF, (1987) Chloroplast DNA evolution among Legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr Genet 11: 275-286. doi:10.1007/BF00355401.
87. Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, et al. (2005) Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol Biol 59: 309-322. doi:10.1007/s11103-005-8882-0. PubMed: 16247559.
88. Stacey G, (2008) Genetics and genomics of soybean. New York: Springer. xvpp.: 407.
89. Wang RJ, Cheng CL, Chang CC, Wu CL, Su TM, et al. (2008) Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol 8: 36. doi:10.1186/1471-2148-8-36. PubMed: 18237435.
90. Goulding SE, Olmstead RG, Morden CW, Wolfe KH, (1996) Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet 252: 195-206. doi:10.1007/BF02173220. PubMed: 8804393.
91. 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. doi:10.1093/molbev/msl089. PubMed: 16916942.
92. Plunkett GM, Downie SR, (2000) Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae. Syst Bot 25: 648-667. doi:10.2307/2666726.
93. Shi C, Liu Y, Huang H, Xia EH, Zhang HB, et al. (2013) Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PLOS ONE 8(3):: e59620. doi:10.1371/journal.pone.0059620. PubMed: 23527231.
94. 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. doi:10.1007/s00122-007-0567-4. PubMed: 17534593.
95. Asano T, Tsudzuki T, Takahashi S, Shimada H, Kadowaki K, (2004) Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: A comparative analysis of four monocot chloroplast genomes. DNA Res 11: 93-99. doi:10.1093/dnares/11.2.93. PubMed: 15449542.
96. Cavalier-Smith T, (2002) Chloroplast evolution: secondary symbiogenesis and multiple losses. Curr Biol 12: R62-R64. doi:10.1016/S0960-9822(01)00675-3. PubMed: 11818081.
97. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF, (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear adh sequences for phylogeny reconstruction in a recently diverged plant group. Am J Bot 85: 1301-1315. doi:10.2307/2446640. PubMed: 21685016.
98. Nie XJ, Lv SZ, Zhang YX, Du XH, Wang L, et al. (2012) Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLOS ONE 7(5):: e36869. doi:10.1371/journal.pone.0036869. PubMed: 22606302.
99. Wortley AH, Rudall PJ, Harris DJ, Scotland RW, (2005) How much data are needed to resolve a difficult phylogeny? case study in Lamiales. Syst Biol 54: 697-709. doi:10.1080/10635150500221028. PubMed: 16195214.
100. Petersen G, Aagesen L, Seberg O, Larsen IH, (2011) When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae). Cladistics 27: 428-446. doi:10.1111/j.1096-0031.2011.00347.x.
101. 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. doi:10.1111/j.1467-7652.2010.00558.x. PubMed: 20796245.
102. Gao L, Su YJ, Wang T, (2010) Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects. J Syst Evol 48: 77-93. doi:10.1111/j.1759-6831.2010.00071.x.
103. Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, et al. (2011) Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome 54: 663-673. doi:10.1139/g11-026. PubMed: 21793699.